I don't know how far you did in terms of BotW, but the way it works burn me out(upgrading gears and inventory slots) so this time around I just decide to dupe stuff. It make the work feel a lot more like a good play ground for exploration compare to really constraint weird grind fest. Let's use your zonite example as material source.

• can you play without farming zonaite and not even upgrade your base battery? Yes, in my early hours without dupe knowledge I managed to unlock all skytower and defeat some harder area mob that defends tower without using anything duped.(I basically started looking for duping because of the reason coming up next.)
• can you finish the game wihtout zonaite gathering? I believe so, it's not even used if you are not using auto build in the over world.
• max battery requires 4500 charges, while realistically without too complex builds that use energy draining components too much, just 45 batteries upgraded should cover a lot of usage. BUT, even that lowers the freedom when you are on a quest to explore "fast". 45 batteries just requires about 1/3 of total amount so about 200~300ish large zonaite. And they give you 1 for quest reward or from chests.
• zonaite charges(the one that fill battery and gives you a bit of red charge even mid using your thing) and auto builds are the supposed zonaite burner. In terms of game design, they want this resource to dump into things that enable you do do something fun or interesting. charges and construct parts are the main thing to exchange capsules. And this is what breaks it for me once I realized how much work I need to do to start feeling freedom building shits and put them to work. If you play it like BotW, it just feels like a side thing that's fun when you have it. But I don't want to play it like BotW, I want to have the freedom to build stuff and use them as I like. Which needs a lot of capsules and a lot of zonaites for autobuilds(when the parts are from memory instead of capsules. )
• since you can't use auto build or capsules in shrines, so getting lots of these dups doesn't break the puzzle. Can you like ride fan-attached machines all the way to destination temples/area without exploring? I guess you can, I don't know since I didn't do that. For my first 2 temples, I still follow quest lines etc.

But it made my korok shipping SO MUCH FUN compare to without duping those charges/autobuild parts. Like it literally changes the boring and repetitive quests(like holding the sign in place ones) into a fun experiment platforms. Duping the parts also make fusing a lot less "punishing" as some of the better parts are required to upgrade as well. I don't have to "conserve" just go whacking and don't get too annoyed like BotW when weapons break. (as most of the damage comes from fusing, not the weapon states.)

Note, I haven't even build homes etc to dup weapons/bows/shields, and it just unlocks the game so much without the gathering grind. (so the old blood moon weapon/material gather runs is no longer needed.) Like, yeah, I really don't have that much free time to dedicate to one game, so if I have the option to by pass any grind mechanics that also doesn't "break" the game, I am gonna just do it.