I just thought it should have been simpler than this and indeed it is.
The reason it is clicking through is just because we're using our own mouse cursors, therefore, the GTN gauge screen click spot (in FS SDK view) is set with 'CURSOR_NONE'. When set like this, the click event is passing through the click spot rectangle down to the window handler. Of course, we do prefer our mouse cursors than the ones defaulting in P3D4 and we can make them dynamic, in colour, and consistent
This is potentially affecting our customers running the sim in full screen with undocked popup windows. However maximized main window or non-undocked popup windows are fine.
I don't remember this but is P3D3.4 offering the 'lock window' menu option as well?
In any case we'll be adding a new window setting for the ini file to let you choose our cursors (with the limitation discussed here) or native simulator hand cursor. This is one great advantage of our technologies:
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