Not the person you asked. But the only thing I can think of, would be how the flatpak's sandbox might cause friction. Most of the time, you won't even notice it. But, once every while, it shows its ugly face.

For example, the situation around native messaging is still a mess. This prevents e.g. your flatpak browser from communicating with your locally installed password manager. While a(n ugly) workaround exists, it's quite maddening that it hasn't been resolved in all these years 😅.