Thanks for your responses. That's a shame but among other things, it gives us more insight on how Curtains works.
However, in my particular case, Curtains is working as designed and there's nothing to fix on Stardock's side. It's the application that's at fault as it makes a tool window that overlaps the titlebar and assumes it knows what the colour should be underneath. With Curtains enabled, it no longer does.
The developer was just looking for an easy way to be lazy and not have to figure out a better solution. I know this with a high degree of certainty as I am the developer .