flatpak distribution is generally done by the developer as a common packaging method. if a distribution wants a native install it’s up to package maintainers of the distribution to support the application. although the package maintainers have to make sure they’re packaging the right versions of dependencies which becomes a problem known as dependency hell.
in your example of handbrake it’s true the main application is pretty small but that’s because it relies on libraries and is a wrapper for ffmpeg. even if you install through a package manager you still need to compare the total size of dependencies.
the disc space usage becomes a problem due to installing libraries both natively and in sandbox. however if you keep a relatively small system install and install applications through flatpak the disc usage will be pretty negligible. if disc space is really a concern then using something like btrfs with compression+dedup would probably solve most problems.
i found the stability is highly dependent on the in game settings. i have a full amd system, cpu+graphics. considering i had an amd card (latest gen) i would disable ray tracing and fsr and most of the time i couldn’t even get past the initial loading screen without crashing. found that setting fsr to balanced and enabling ray tracing to lowest settings would let me play for 4-5 hours before crashing. I’m on Linux so most likely still need to play around with the lighting options for better Vulcan support.