im not 100% but i had a problem like this once i had a standard alarm and fitted an aftermarket alarm too , the problem was that i had to disarm the 1 first and arm the other first or the 1 would affect the other and set it off ,i.m pretty sure that if you are not happy with the standard alarm then a reputable alarm installer could disable the factory one and install another 1 of your choice, then reverse the procedure when you sell the car.
yes as when you fit an alarm you pnly tap onto the cars lock and unlock wires. Does the bmw alarm have a seperate key fob if so what does it look like? (pic?) there shold not be a problem but i can tell you from seeing the key fob