Hi,
This is still a problem on Ubuntu 20.04 with X2Go Client 4.1.2.2 connecting to XFCE through x2goserver 4.1.0.4-0~1914~ubuntu16.04.1
If I put both my local gnome panel and the remote XFCE panel at the top, then the top pixels in remote desktop cannot be clicked (tool tips work).
If I put my local gnome panel to the left, then only the top left corner pixels of the remote top panel have the problem (which is where they intersect).
If I switch my local desktop environment to XFCE, no matter where I put the panels, it always work.
Cheers.