Update: I don't know if this will help anyone in the future but I figured I might as well post a work-around I found. If I make my popup on overlay a "popup group" with another small no-fill popup in an obsolete corner. Making it so I have 2 popups on overlay. Instead of trying to /close my popup on overlay I can just open the other no-fill popup instead. Thus forcing closed the original cumbersome popup on overlay and trading it for a much less intrusive one.
I do this by adding a hotspot jump link on each overlay set to "in view" with the syntax "jump://overlayname/nofillpopup".