They are certainly different things, but they're not unrelated. The inability of the user to change the system trust store is part of why certificate pinning is no longer (broadly) recommended.

A lot of mobile software is just a UI around an external web API. The main reason why Android makes it difficult to get the OS to accept an external certificate (you need root for it) is because without it, you can just do a hosts hack through a vpn/dns to redirect it to your own version of that API. Which app manufacturers want to prevent since it's a really easy way to snoop on what endpoints an app is calling and to say, build your own API clone of that app (which is desirable if you're say, selfhosting an open source server clone of said software... but all the official applications are owned by the corporate branch and don't let you self-configure the domain/reduce the experience when you point it to a selfhosted domain).

It's extremely user-hostile since Android has a separate user store for self-signed CAs, but apps are free to ignore the user store and only accept the system store. I think by default only like, Chrome accepts the user store?

Most software is tools of control and exploitation, and remains in an adversarial relationship with its users. You give software to users to make them make money for you; you protect the software from users so they don't cut you out, or use software to do something you'd rather they don't do.

Software that isn't like that is in a minority, and most of it is only used to build software that is like that.

For example, to make it harder to reverse engineer the protocol between the app and the server.