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.
basically no company wants the bad PR. If it had come out twitch would be known as the platform with pedos and parents wouldn’t let their kids use it resulting in the platform becoming obsolete.