I don't know if I ever noticed the shoulders in the RotS/TCW scenes or if I just made myself forgetFor the Eta Interceptors in ROTS, you can actually see the droids' "shoulders" sticking out of the slot, so it's not extended domes. I think some people theorised that the droids had telescoping legs in order to make them fit.
So both styles of Jedi Starfighter just have nowhere to put the droid body? That seems a bit mad. Has it been an issue over the years with fans?
I see that Filoni was able to correct the issue on the first style in TCW by moving the droid socket.