Fair enough. I have been there myself.
But Universal Blue are not immutable OS offerings. They are atomic desktops - sort of in the middle. Not the kind of immutability that one might take advantage of in a classroom setting (for example) where the machine reverts to a known state upon reboot.
Rather it takes the stance that the host OS is off limits for modification deferring to delivery via bootc images. Anything done by a user (where even sysadmin is a type of user) should be done in container technology of some sort.
I wrote an article here to help summarize - Did You Know? How ostree update merges changes into etc and var
And as @red11 mentioned, a lot of the problems you are experiencing can be simply solved by switching to dev mode where many things you might be looking for are installed by default.
The other option is to craft your own bootc image via GitHub - ublue-os/image-template: Build your own custom Universal Blue Image!.
Then you have complete control over the bootc image you use (and deploy across an orginization). In the Containerfile you will not have the atomic desktop constraints; can work with copr’s as usual, etc.
I hope that helps.
I am excited for the journey you are on. Good luck!