With an aftermarket starter/alarm they may be able to program the lock features. When we install an aftermarket remote starter the remote starter door lock/unlock feature is connected so it will work when the car has been started remotely. You can walk up to the remotely started car while it is running and use the aftermarket fob to unlock the doors. After you press the button to turn off the engine with the aftermarket fob, then you can use the Toyota remote that came with the vehicle. Lock and unlock the doors with the Toyota remote with the engine off.

So, we program the systems so they operate independently and when one is engaged the other will be off. It becomes complicated with 2 remotes. If you are only using an aftermarket fob then it will be much simpler.