Pretty sure the issue stems from the added checks to see if the selected unit is a settler. I didn't look that closely, but that seemed to be what was changed in the GEM version of CityLimits. I copy/pasted everything from the original CityLimits from below
cityPlots = {};
borderColor = Vector4( 0.98, 0.9, 0.55, 0.5 )
to the end of the file into the GEM version and it went back to working the way it used to. It shows the city limits when you select ANY unit now, of course, but I'm fine with that.