I assume this is based on an experience with Kinoite? Am I right?
anything that involves changes to the system
I’d argue “anything” is too harsh. But yes, there are definitely edge cases that are either very/too cumbersome or outright impossible to achieve on Fedora Atomic.
However, I’d argue that while the associated paradigm shift and learning curve do require some commitment to adjust to, it is a more sane way of running a system for most people.