I can't speak for GP but the number one reason I prefer my distro's repos over flatpaks has nothing to do with Flatpak as a technology.
Most distros have a fantastic track record of defending the interests of their users. Meanwhile, individual app developers in aggregate have a pretty bad one; frequently screwing over their users for marginal gain/convenience. I don't want to spend a bunch of time and energy investigating the moral character of every developer of every piece of software I want to run, but I trust that my distro will have done an OK job of patching out blatantly user-hostile anti-features.