The GSX installer will only patch the "vehicles_airport.BGL" if it's the original unmodified version from Microsoft. If it founds a modified file, it will give you a warning, and will not patch it.
However, this won't cause big problems, the only reason to patch that file, is to remove the default pushback truck so, the only possible side effect if you have those 3rd party ground vehicles installed, is that you might see two pushback trucks, the "default" (which is not default anymore, since it has been replaced by those products) and the GSX one.
But other than that, there will be no other side effect because, the GSX Pushback routine is independent from the FSX one, so you won't see two pushback truck pushing your airplane, the default one will just stay there on the parking.
We might improve the installer in future updates, to recognize and patch any possible version of the vehicles airport .bgl, but it will always an option to remove the pushback truck, if the .bgl is not default anymore, on the assumption that if someone has took the step to buy a 3rd party product to replace the default vehicles, he would like to at least being asked when something is going to remove one of them.