Same for me. I had really weird stuff to debug. Could not save from FF to /tmp for instance (and I really like that for downloads I should use immediately and can be removed).

I found Keepass to be a snap/flatpak once: so many extra layer of complexity for a passwrd manager? No way that's good for security.

What about transactional updates? Applications might have undefined behavior if their libraries or other assets are changed under their feet.

If there's a security issue, I want to be able to update libraries and such independently of applications rather than waiting for the application devs to do it.

I don't think it's caused a problem for me in the last 10 years or more. It may have and just forgotten about it, though. If it happens, it's not a huge problem to fix it.

Yeah. I can never seem to get the fonts to work with flatpak/snap Firefox. Seems kind of essential.