The colors of these things are controlled in the DLL (and displayed by the executable, not in the Python for the interface - these functions are not even exposed to Python). The object itself is called the city billboard. (I have no idea how the mod that makes these bigger works... It may be a purely graphical change, in which case it would just be modified art files.)
The colors are set in CvCity::getCityBillboardSizeIconColors. In regular BtS it uses the growing/stagnant/shrinking color for the background and black for the text if it is owned by the team of the player who is looking at it, and the civ's primary color for the background and secondary color for the text otherwise. So to make it use civ color for the player, you'd just wipe out the whole "if" check for the city owner's team being the active team and just go with what is in the "else" block of that code. And then recompile the DLL, of course.