Hi, welcome
That looks like a very useful script. Well done
Thanks! I made a slight mod to the script this morning (ha!) so that it runs the python in a Terminal window. That way you can see a bit more of what it's doing. I think if you've already done some of this stuff manually, it might complain about replacing files or what have you, so in Terminal at least you can tell it what it needs to do.
Again, this is for the Steam version only. I could try to write in App Store support but would have no way to test it. Anyone comfortable with scripting can open the app package and edit Contents/Resources/Scripts/civ5enablesteammods.py.
Civ5_Enable_Steam_Mods.zip