THIS is the issue, the issue with almost every paragraph of your comments that I've read.
Your assumption that everyone cares about this is false, there's no "misconceptions" here. The only misconception is the one that GNOME is the center of the Linux universe... which is tacitly untrue. GNOME is an extension of a modular system, one that was also designed to be built upon to create better experiences. GNOME once also shared that sentiment of modularity, and it worked perfectly fine for it: GTK2 and GTK3 both respectively inspired several desktops to exist purely based around their design languages, and worked pretty much flawlessly. If the GNOME team is scaling down their ambition and deciding to be less modular, then fine: let's put the tiger on the table and yell at it. You can publicly say that you're distributing with Flatpak because you're too lazy to debug a native version, I won't take any umbridge. I'll just compile the app myself and use it as normal, no skin off my back.
The ultimate Achilles heel of Flatpak is that it will inexorably always be a second-class package manager. You'll never install it without having another, feature-complete package manager operating alongside it. The UNIX philosophy is to do one thing and do it well: Flatpak tries doing a hundred things, and can't do a single one better than another, dedicated tool. There is no argument here. Flatpak is not, cannot, and will never be considered a real package manager. It's a second-class supplement at best, and abhorrent bloatware when it stops working properly.