Bazzite's messaging has merit, but we'd be making a mistake by regarding it as absolute. It makes more sense to take them as carefully written guide lines for a specific audience.
Furthermore. with all due respect, but OP's writing doesn't imply installing/managing software with rpm-ostree. Which, is actually the subject of the documentation entry you quoted. As such, I think you might have misunderstood them.
Youre breaking a core tenant of immutable distros by installing system level packages.
Finally, FWIW, I absolutely disagree with the above. The page you quoted from seems to agree with me on this: "Layering packages are mostly intended for system-level applications, libraries, and other dependencies."