Toyo Svc replacing after mkt alarm on venza with alarm. Will I have problems?

Depends on who/how the aftermarket alarm was installed. If it was rushed and hacked into the wiring system then unless toyota is allowed to put wiring and other affected devices/controls back to original condition then NO they should not warranty it (unless the aftermarket system was installed by them originally).This process will not be cheap but IF you have a reputable dealer then you should end up with a Venza that's dependable for a very long time (with proper care along the way)