Kerbal Space Program

It's a known problem that clicking on a window will let the click fall through to anything underneath. This is most noticeable with mods, although it might also be endemic to some of the stock windows.

I released a fairly simple mod which solves the problem by providing a wrapper for the GUI.Window and GUILayout.Window calls, the link is below.
I don't know if this will be helpful, but if there was someway you could override the stock calls and use this, it would solve a lot of issues that people have with this.

https://forum.kerbalspaceprogram.com/index.php?/topic/170747-131-click-through-blocker/&tab=comments#comment-3291957