Well as far as I'm concerned, all scripting screen coordinates should be in absolute coordinates and if they aren't, it's a bug.
I doubt I'll have it fixed by 3.6.9 release, though, the branching thing has been an utter pain in the ass to work with. Before I commit anything more to that branch I need to set up another dev environment for it, I've tried having a separate branch on my HDD and it hasn't caught one completely by-itself difference in lua.cpp. I've already been yelled at for not test-compiling, after fully testing and test-compiling changes, because I let that one little bit slip through when I committed to the 3.6.9 branch.