Apps also change and disappear, especially if you get them from a store.

Not if I have the apk, or the app itself installed to my phone.
There's also websites that keep archives of different versions of apps, and you can verify that they didn't tamper with it by comparing the APK signature

I don't want a retailer like IKEA to run code on my device

Does their website work with JavaScript disabled? Most such websites don't.

But I agree that the unreasonable mandatory apps to be able to use services must end. IKEA and everyone else should just give order tracking information on their website.

Why would you uninstall an app that you use to manage system settings

Because it's for a very specific thing that I don't often need.
Or because it was useful in the past, nowadays I don't use it, but I don't want to lose it either, in case I want to use it in the future. Because I don't want to rely on the store still having that app, on the app not being enshittified, on the store search not hiding it, on me finding it again...
Some examples: wallpaper setter app, because without it is often impossible to set it tastefully for some reason. Several kinds of process managers all with different unique functionalities. Debugging apps like for push notification testing (I have at least 2-3 dozen of these). Several kinds of networking apps (this and that vpn, proxy, tor, network scanning and debugging tools for when I need it), app for the occasional storage cleaning, app for mounting iso file on phone as bootable usb for a PC, several apps that set a hidden but persistent system setting once, archive (think zip) managers apps, several for picture editing because they all have different useful functions (and these are not even for photo effects), a dozen mapping related apps that are not relevant in half the year.

Why would I uninstall them?
Because on top of storage, they cost a lot of other resources. For share dialogs I have ~8 pages of handler apps, which slows down the share dialog from opening, but also slowing down me from finding the right action. Most of these aren't even useful, if I could I would toggle them off. (Maybe this would be a good project idea for improving LOS one day...).
A lot of apps have dozens on dozens of broadcast receivers, services, content providers that are all registered into the system, and slow it down in a death-by-a-thousand-cuts way.

especially if you want to rely on the Play Store to get it back?

You misunderstood me, I don't. I avoid the play store as much as I can. I make a local backup before I uninstall the app if I don't need it, even with apps from f-droid.