it’s great for applications that are notorious for requiring specific versions of libraries and can cause dependency hell. moves unnecessary system dependencies into a sandbox. for me this means i don’t have to enable multilib to install Steam and pull in 32 bit libraries on my root.
while it does take a lot of disc space it doesn’t duplicate dependencies in most cases. i would say you receive some good benefits at the cost of a bit more disc space, such as increased security, easy installs, explicit app permissions. it’s great for when you have to install a proprietary tool in that you gain control of what it’s allowed to access.
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.