https://docs.bazzite.gg/Installing_and_Managing_Software/rpm-ostree/
Layering packages irresponsibly can be destructiveand may prevent updates as well as other issues until the layered packages are removed.
Use this method as a last resort and for anything at a "system-level" only since it can pause updates, if the package contains dependency issues with future upgrades, until the package is uninstalled.
MAJOR caveats using rpm-ostree¶
Layering packages can cause severe consequences including:
- Pause system updates until package(s) are uninstalled.
- Prevent rebasing to different images until package(s) are uninstalled.
- Conflict with existing packages as part of the image leading to dependency issues.
- Updates taking longer to download as you layer more packages to your system.
Youre breaking a core tenant of immutable distros by installing system level packages. i think that might be your misunderstanding?