There was already a post on this. Basically the argument about home is true but this is because 1) apps should not use filesystem access but rather portals (if they can) 2) nothing should be executable in the home folder (nobashrc, no script, etc...)

If I remember well the second argument was about update not being frequent enough.

So nothing fundamentally about Flatpak but more about the infrastructure (lack of updates) and the use of it (we should not allow home access and use Portals or we should disable bashrc).