"You get /var/snap and thats it."
Flatpak can have similar issues. I've been using monodevelop in flatpak, and it includes /usr/bin/perl, which hides the system /usr/bin/perl with external commands, which means I can't use any CPAN modules. Whatever the app packager decides in terms of sandboxing, that's what you're stuck with as an end user.
For now, I still think AppImage kicks flatpak's butt all over the place. I suppose that could change now that it's trendy. :/