Games

Depends on what the average user wants to do, here's a list of random things off the top of my head that require system wide changes, i.e. they will get overwritten with the next update (which btw means you'll need to do these at the very least monthly, but might be daily if you also want the latest SteamOS updates):

• Configure a Logitech gaming mouse, while the program to do this (piper) has a flatpak, it depends on a library (libratbag) being installed system-wide. There are technical reasons for it, but in short it means it doesn't work. This is not a problem on most Linux distros because you can just install libratbag using your package manager.
• Use something that's not KDE. If you wanted to use GNOME, XFCE, i3, or whatever else, you couldn't. You're stuck with KDE, if you find a way around it better automate it, because next update it will be gone.
• Plug non-standard stuff that requires custom udev rules, e.g. using ADB on android phones. If you want to install things from your computer onto an android phone or of you want to root your phone you need to use ADB on it, however ADB depends on some udev rules for some android devices to be properly recognised, most distros have a package called android-udev-rules or something similar that has those configurations.
• Change your boot manager. Doing this is likely to fuck up the deck, since the next update your boot manager will be deleted but the standard one might not get reinstalled. I don't know exactly what would happen, but my guess is that every update you would need to either go to the bios to temporarily set the old boot manager back, or boot using a live image and reinstall your boot manager.
• Change kernel parameters. There are plenty of reasons to want to change your kernel parameters, and whatever changes you make will need to be redone every update.
• Install custom kernels.
• Install firmwares.
• Install drivers.

That's just what I came up with half-asleep in 5min, I'm sure there are plenty of more examples. Yes a user might go his entire life without needing any of that, but someone who doesn't know Linux will get frustrated if he needs any of it and nothing that he does work and when he gets it to work it's reverted the next day. On the other hand, someone who knows Linux doesn't need to be told any of this, because they understand the limitations and why they exist, and can work their way around it, but most importantly probably wouldn't ask if the steam deck can be used as a PC or if it's proprietary, since the steam deck in kind of a big thing in the community.