Let’s be more specific: some Flatpak applications/runtiles will be uninstalled. This does not touch packages installed as rpms in any way.
Yep. Read man flatpak-uninstall and see what it says for the --unused option. And of course, your system in general uses software and libraries that are not installed as Flatpaks. You should read up more on Flatpaks to understand how they work. Some resources here:
What makes you think that? (Also note that the gnome 3.36 runtime is not being removed—probably because it’s in use by these).