Oh you mean for command line applications, yes, Flatpacks cannot do that yet. Personally I manually enable Snaps in the distros I use, as some apps only exist there, but have been orienting myself where I can limit the exposure to only the packages I want.
You made me chuckle :) True, if coming from macOS, Gnome can be familiar enough but the defaults are terrible. Even those used to Macs need to install/enable the basics like maximise/minimise buttons etc. I don’t understand why even a Gnome centric distro like Fedora doesn’t come with Gnome Tweaks installed by default… Let alone the fact that usually the average user will also install a bunch of extensions. That is why Ubuntu is arguably the one doing the better job out of the box: their Gnome is actually useful from the get go.
You are probably right but some of them are worth very little now… possibly more useful as test devices or to run proxmox on it and run some containers