I’ll add my 2 cents to your very well written comment.
My biggest gripe with flatpaks notably, is the more difficult integration into the system. I use about a dozen flatpaks, and for every single one I had to tinker with flatseal to give them the correct access permissions, that I had to research online. One specific flatpak coulnd’t even work with those additional permissions. Half of those flatlaks also will not follow my system theme and their GUI looks broken or out of place.