I’m glad to hear that you found the most egregious culprit. Hopefully you’ll be able to get it to work after your subscription list ‘functions’ (again). (I’m honestly completely oblivious of what this software is or how it works.)

Though, if you allow me, I would like to give some comments. So, without further ado.

Throne came up with another error, it was unable to change file ownership in /usr directory

Hmm…, curious. I would think that it shouldn’t even (necessarily) require anything like that. And, if it does, perhaps the maintainer/contributor should be addressed in hopes of resolving the issue; I’m sure they can figure out a workaround (or so).

(of course it couldn’t, it’s an immutable system)

😅. This is actually a very nuanced topic:

• Bazzite has for example made plenty of changes to /usr compared to its upstream; i.e. Fedora Atomic. So, there is a supported way of doing this in order to create an image with the desired changes to /usr. If you got any such needs, consider taking a look at this page of Bazzite’s documentation.
• Furthermore, instead of making changes to the content of folders like /usr/etc, /usr/share et cetera; one could instead make changes to the content of folders like /etc ~/.local/share et cetera.
• If you only want to write to /usr once and would like for said changes to not persist after a reboot, then commands like rpm-ostree usroverlay and bootc usr-overlay are worth mentioning.

So, to be clear: while it is true that Fedora Atomic does not like/support making changes to /usr at runtime, it’s not like it’s necessarily limiting you if you really desire to make changes to /usr. Even if non of the methods 100% function like how sudo <input change> /usr/<some content> would on a traditional distro*.

Thanks a lot for so much effort figuring things out!

It has been my pleasure 😊!