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Are you sure that any of the flatpak-based browsers actually run in Wayland. For the longest time they had to be explicitly enabled to work with Wayland and not X11. Even very recently both Brave and Edge required flags to run Wayland (and maybe still do); though Chromium-based even require specific flags to enable the two-finger swiping for navigation;
--ozone-platform-hint=auto --enable-features=TouchpadOverscrollHistoryNavigation, as can be found on the ArchWiki. As for the ones based on Firefox, they should work right out of the gate. If they don't, then first check if it's running on Wayland; perhaps running theflatpak override --env=MOZ_ENABLE_WAYLAND=1command in terminal already solves that issue, however this should have been enabled by default. If it continues to not work, then -after ensuring that you are in fact running Wayland- you should make a bug report as this isn't intended behavior.