Suggested by Darin's comment in bug 68402, I think WKView suffers from a similar issue. I need to make a sample app to verify, but based on code inspection I think WKViews will always be inactive in NSPopovers.
Created attachment 107995 [details]
I think this is all WKView needs. I still need to test this.
Comment on attachment 107995 [details]
Approval conditional on whether your testing shows that this actually addresses the problem, of course.
I am using a WKView in an NSPopover, and I can confirm this patch works.