Ooh, Metal Gear Solid is another one I've been meaning to play—it seems to be the kind of series that people get really invested in. And I definitely intend to play Majora's Mask next! I've heard it can be polarizing, partly because of the time limit mechanics (I only vaguely know that it's three days, but you can reset it or something? Guess I'll find out in due time!), and also that it's darker than OoT. I truly know almost nothing about Majora's Mask, so I'm really excited to go in and experience it for myself!
There is no permanent lockout in this game.
Phew, that's a relief! Part of why I was constantly scouring Hyrule for every last collectible is that I thought you could miss items (although I'm also just a completionist); perhaps I'm misremembering something I heard about another Zelda title, or I just imagined it entirely. With that, after a tiny bit more cleanup, I went forward with the story with confidence, so thank you for disabusing me of that misconception!
Caveat
I missed this when reading the comment for the first time and you suspected correctly—I did not realize what the lock was (maybe you can't immediately place the Master Sword back in the pedestal to go back?)
I find the secret holes very picky
Can I just ask point blank:
Secret holes
are all instances where the Stone of Agony activates secret holes? Because besides that Goron City trouble, I also could not for the life of me bomb open secret holes in these locations:
- Left of the Lost Woods entrance
- Stone circle in the westmost part of Zora's River (the bit entered from Hyrule Field)
- Platform in Zora's Domain pond
- Ground in the Sacred Meadow near the Triforce platform (I did open the one before the maze, though!)
It does seem a bit picky, but the ones that I did open only required maybe two or three bombs, which is what makes me wonder if there's another mechanic. No need to reveal the other mechanic yet if there one, but it'd be helpful to know so I can save myself some bombs and some time.
Lost Woods
Oh, I knew where the entrance was, but I hit what I thought was a dead end because I was relying on what I think is a visual artifact not seen when playing on console: the paths between rooms are pitch black, whereas you can actually see the triangles in the ones that lead you out of the Lost Woods. But when you're going to the Sacred Meadow, it also has the triangles, and when I went through the wrong one (a two in three chance) and it spit me back out, I assumed I was in the wrong place and just gave up...very silly, in hindsight. You don't have the musical cue after the first time as far as I could tell, so I just had to guess. And I made a proper flow chart so I can easily make my way through again if need be!
...oh wait you covered the visual distinction in the next spoiler lol. Although maybe this bit was edited in, because I don't remember seeing it the first time.
Also, I did make extensive use of the "call Saria" feature—I guess it's meant to tell you how to progress, but I was mainly using it for roleplaying purposes.
That info is in the save file, and Ship of Harkinian can show you how many there are and how many you have, but it also names every region and dungeon...
Ah, I guess I'll hold off until I'm doing the endgame cleanup, then. As it is, I'm already up to forty-odd Skulltulas and plenty of extra Heart Containers, so I think I'll be okay.
It's the other thing in the Water Temple that scares me :scared: I recommend filling all your bottles with Fairies... 

Rundown of my experiences since the last comment
So, like I said, after a bit of cleanup (including getting Bombchus) I went ahead and leapt forward through time (or...I guess, went into stasis?)! I actually got goosebumps when I opened the Door of Time and stepped across the threshold—proof that you don't need raytracing and 12K textures to create a mood. I'm not sure if I got all the lore, though, and after my confusion, I've finally decided to switch to English for the remainder of the playthrough. I know this isn't exactly highbrow literature, but I still want to make sure I'm not missing any important story beats or lore dumps. Given how much I'm enjoying this, I'll very likely replay it in the future (maybe a Master Quest run?) and I can always flip things then, playing in English for the Young Link section and Japanese for Adult Link. Hopefully my reading speed will have improved by then so I'm not scrambling every time auto-advancing text pops up...
Anyway, I immediately ignored Sheik's recommendation that I go to Kakariko Village and went wandering all around. I was pretty shocked by just how grim things were—I did vaguely know that some things were in ruin, but the ReDead in the town square caught me off-guard as did the maelstrom over by the castle. I think the first thing I did was go to Goron City, where I got the Goron Tunic and Giant's Knife, and then I headed over to Zora's Domain, which I was surprised to see had iced over (and where I promptly broke my Giant's Knife on a wall, it never having tasted the blood of my enemies). I tackled the Ice Cavern, making a note of all the currently unreachable Skulltulas and filling all three of my bottles with Blue Fire. I used one of those to free King Zora and receive the Zora Tunic, although not before testing my new Iron Boots in Zora's Fountain on the way over and immediately drowning...whoops.
After that, I heeded your advice and went to Lon Lon Ranch, where I unseated the comprador Ingo and got Epona pretty easily but then took an embarrassing number of tries to clear Malon's trial (maybe a half dozen, and I just squeaked by with a second to spare). Sure, BotW's horses are lovely, but seeing as you already have fast travel before you get one I think Epona in OoT still has the greater impact! I went to Lake Hylia and Zora River to check on what I thought would be beanstalks but actually ended up being moving platforms—definitely a surprise!—as well as learn the Scarecrow's Song (thanks again for saving me some tedious backtracking!). I then went to Kakariko, where I talked to everyone and collected everything that I could (including the Hookshot and multiple Pieces of Heart). After going back to get my Ice Cavern Skulltulas and entering the Water Temple for about 5 seconds before coming to my senses, I returned to where it all started: Kokiri Forest.
Again, I was pretty surprised by how my home had become such a hostile place! After visiting my trophy cow, riding the weird bean platform in town, and paying my respects to the Great Deku Tree, I finally made my way to the Lost Woods, which I carefully mapped out as mentioned earlier. I was surprised to be attacked by the Skull Kids, but it seemed to sad to fight them, so I just ignored them and hurried onward. Both the bean platforms I encountered in the woods seemed fairly pointless: there's one that takes you above the bridge to Kokiri forest and one that puts you up on a ledge in the Business Scrub room where there are no items to be found. Am I missing something?
Anyway, after taking an embarrassingly long time to get through the maze, I finally started the Forest Temple, and...boy, was it harder than I'd expected! I knew the dungeons would get more complex, but there were multiple points where I got stuck for a bit, and I also now realize how useful Farore's Wind is when you hit a door that you don't have a key for but want to be able to return to it quickly to keep progressing. I won't bore you with the details (other than that it took me way too long to realize I was supposed to shoot the portraits), but I eventually made it through, and after dying to Phantom Ganon once (in my defense, I went in with like 5 hearts and no healing items!), I successfully vanquished him. Suddenly seeing Ganondorf was definitely an "oh shit!" moment, since I assumed it be some unrelated thematically appropriate boss. And while I did get a bit frustrated at points in the dungeon, it was very satisfying to clear it all out!
I'm definitely glad that I RP-visited Saria one last time in my previous session because I was gutted to find out that Saria had become a Sage and would be forever separated from Link from then onwards. Again, I know that the writing isn't super deep (Saria cheerfully says that she's glad to be helping you save Hyrule when you call her afterwards), and maybe I'm just a sucker for this stuff, but it hit me surprisingly hard. And the Mido's dialogue after that...my heart!
After recovering from that emotional blow and chatting with the rest of the Kokiri, I returned to Kakariko to claim the 40x Skulltula reward (it just said "Bombchu", but I think it was an upgrade from 20x to 30x capacity?). I also did the fetch quest (which was a breeze, thanks to obtaining Epona early) to get the Poacher's Saw, which was darker than I expected (poor guy, I was really rooting from him the moment I met him as Young Link...), and I was also sad to see that despite me never laying a hand on them, the Skull Kids didn't return to the Lost Woods, not even after I played Saria's song on their stumps. But on the bright side, at least the Deku Tree has been reborn!
Obviously, I don't expect you to reply in any detail whatsoever to my summary of my playthrough, but I just thought it'd be fun to share (and it was also a nice way for me to reflect on the day's progress). I've probably been playing a bit too much, so I'm going to try to dial it back a bit and savor the rest of the game.