That’s not how Flatpak works.
Flatpak has runtimes, which is where most shared libraries are. There’s a common base one called Freedesktop, a GNOME runtime, a KDE runtime , an Elementary runtime, and more. (The GNOME and KDE ones are built on top and inherit from the Freedesktop base runtime.)
https://docs.flatpak.org/en/latest/available-runtimes.html
Additionally, at least for Flathub, they have shared modules for commonly used libraries that aren’t in runtimes. (Many are related to games or legacy support like GTK2.)
https://github.com/flathub/shared-modules
Lastly, some distributions are building their own runtimes and apps on top, so the packages they build are available as flatpaks as well. This is the case for Fedora, Elementary, Endless, and others.
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/