Well of course If conditions will be difficult if there are two jetways at a gate and they will get in conflict with each other. But If you asign only one door connection to each jetway, even though there would be the possibility to select two door connection point for one jetway there won't be any problem, so you don't even have to check the amount of jetways at gate. You just have to put a notice to the manual somewhere, to set only one door point for multiple jetways.
But if only have one jetway and it would be possible to set up two door connections, there won't be such problems interfering only in Auto mode. As I understand correctly the logic now is something like this: Flying the A320 for example leads plug in to look for jetways assigned to LF1, but finds LF1 and LF2, LF2 not possible for aircraft, so it greys out the jetway LF2 connect button or in auto mode will auto connect to LF1. (I don't see a problem here). Flying the A330, it will see LF1 and LF2 in vincity, shows up both connection buttons and user can choose which door to connect (no problem so far to my mind). Only in auto mode plug-in won't know to which door to connect.