Will llook into it. However I dont use Linux, so I might not be any help.
Viewing post in Legend of Shadow Hunter jam comments
It is just I wouldn't disregard the possibility that Unity or Itch use not fully compliant methods to cut development time or whatever. In this case some settings/HTML shell/Javascript tweaking might be needed.
Unfortunately I haven't tried to make a mousegrab in my Godot to test things so i can't tell what exactly might be going on under the hood.