To be clear, this was a configuration bug on Whonix’s side, not a problem inherent to Wayland. No one else ran into the bug and reported it, and we didn’t notice it. That’s why bug reports are valuable
Switching to Wayland is not an end in itself, there are concrete security advantages (unrelated to the typical “apps can’t spy on and control each other” advantages) that come with it. Beyond that, X11 is (semi-rapidly) dying. See: