As I understand it from that bug report, the problem is that the Windows app doesn't have to provide any link between the menu or tooltip and the window it's from that's visible to Wine. So your solution basically boils down to modifying every Windows app out there to make it Wayland-compatible, potentially including a bunch of niche industry-specific or even company-specific ones.

There's a similar problem with implementing X on top of Wayland, and so XWayland has special powers that normal apps don't in order to be able to work. That's why running Wine as an X client under XWayland doesn't have this problem.