1. In a leased vehicle situation, they may be penalized for drilling holes.
Although, you're in lubbock, so I bet a bunch of the ones you see are oil/gas which probably have 1 or 2 NMO mounts anyway, so they "should" do it with an NMO... but chances are they buy the wilson kits in bulk from wilson and go with whats in the box VS ordering a NMO version.
2. The "right" way of running thru the third brake light is to order a second gasket (provided that the original has one) and notching it for the cable, then putting it all together, or using clear silicone to make a gasket with a notch for the cable. That way the cable isnt pinched by reinstalling the third brake light. Also, ideally, you should run the cable thru the bottom of the third brake, not the top, so you can be assured that rain wouldnt get thru.
Cant do that with thicker coax, but the RJ174 on the mag mount wilson antennas, or the thin cable on a mag mount XM radio antenna can easily be run this way. Short install time, short deinstall time without permanent modifications.
Just because you or I NMO everything, that doesnt mean that is the correct way for the entire world to do it.