Yeah, that’s a big, weird if though. Most modern apps can rely on the runtimes for their dependencies and not have to ship their own custom dependencies.
It’s different from something like AppImage, where everything is bundled (or Snap, where a lot more needs to be bundled than a typical Flatpak, but not as much as with an AppImage).
Additionally, there’s always some level of sandboxing in Flatpaks (and Snap packages) and none at all for RPMs, Debs, or AppImages.
Also, Flatpak dedupicates common files shared across flatpak apps and runtimes, so there isn’t “bloat” like what you’re talking about.
https://blogs.gnome.org/wjjt/2021/11/24/on-flatpak-disk-usage-and-deduplication/
GNOME 46 (currently in release candidate mode and fully releasing later this month on March 20) is adding support for remote graphical logins via rdp:
https://9to5linux.com/gnome-46-to-introduce-headless-remote-logins-via-gnome-display-manager
So you’ll be able to do this pretty soon, after upgrading.
It’ll be in Fedora 40, scheduled for release around April 16.
https://fedorapeople.org/groups/schedule/f-40/f-40-all-tasks.html