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This seems to work well for me too. I've had to do a few things:
Give it access to the Wayland socket flatpak override --socket=wayland ...
Copied the .desktop from ~/.local/share/flatpak/exports/share/applications/com.logseq.Logseq.desktop to ~/.local/share/applications
Swap the Exec lines around so the default one becomes Wayland
I changed it to use --ozone-platform-hint=wayland instead of the older --enable-features=UseOzonePlatform --ozone-platform=wayland incantation. But either works.
The shenanigans with the .desktop file was necessary, otherwise I always have to right-click on the launcher and select "Wayland backend". Which makes launching it annoying, and at least in Gnome Tweaks I can't select any alternative desktop action for a startup application.
Wayland support seems fine in my experience now, it would be good to turn it on by default to get more eyes on it to fix any outstanding issues.
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