The baseline tools, like all the GNU standard Unix tools, and other command line tools are still managed by DNF, APT, whatever, and then another set of apps are managed by Snap. It's pretty confusing, especially if you never use the "app stores" otherwise. You quickly end up with: apt install <some command line tool> and apt install gimp, but now that's a different Gimp than the one in App Store. You also can't really remove Gimp from apt, because it's weird that apt can't install everything.
I haven't really used Flatpaks, but Snaps is confusing (to me at least), because it's doesn't actually replace APT and pollute the output of "df" and "mount".
I'm also concerned that some packages will never be updated, or stuck on a library with security issues. Perhaps that me, but I'd rather that that one application breaks.