I don't doubt it, but this is a good place to start.

This claim has interesting phrasing:

Adding X11 sandboxing via a nested X11 server, such as Xpra, would not be difficult, but Flatpak developers refuse to acknowledge this and continue to claim, "X11 is impossible to secure".

If you look at the GNOME post, you'll see they haven't argued against including a nested X server at all:

Now that the basics are working it’s time to start looking at how to create a real sandbox. This is going to require a lot of changes to the Linux stack. For instance, we have to use Wayland instead of X11, because X11 is impossible to secure.

I'm not saying they haven't refused to acknowledge this elsewhere, but it's strange to point to this blog post which acknowledges that the sandbox is very much a work-in-progress and agrees with Madaidan that X11 is hard to secure.

Does Xpra provide better sandboxing than XWayland? If not, I think the Flatpak developer's solution to this is: just use Wayland. And obviously, there's plenty of room to improve with the permissions Flatpak does offer.

I did some searching on the Flatpak Github for issues and found that you can actually use Xpra with Flatpak, and the answer is "just use Wayland":

• https://github.com/flatpak/flatpak/issues/3833
• https://github.com/flatpak/flatpak/issues/3684

This is also concerning:

As odd as this may sound, you should not enable (blind) unattended updates of Flatpak packages. If you or a Flatpak frontend (app store) simply executes flatpak update -y, Flatpaks will be automatically granted any new permissions declared upstream without notifying you. Using automatic update with GNOME Software is fine, as it does not automatically update Flatpaks with permission changes and notifies the user instead.

Source: https://privsec.dev/posts/linux/desktop-linux-hardening/#flatpak

It's great that GNOME Software notifies you when permissions change! I don't use Flatpak enough to know, but I hope flatpak update notifies you too if you don't use the -y option.