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.

For Flatpak, I use vscodium to strip Microsoft telemetry out of vscode.

It works really well, the one downside is that vscode extensions are pretty intrusive. They expect system provided SDKs. So you then have to install the SDKs in the Flatpak container so you have them. If vscode extensions were reasonable and somewhat sandboxed that wouldn't be a concern.

All that is to say, Flatpak works well for this purpose too.