I'm going to have a Viper 791XV installed on my car next week, but after I left the alarm place, I thought to myself that I would like to have it so that when I un-arm the car, only the driver'* door unlocks. It would be a little safer like that I think.

Is there a bypass or a switch that can be installed to allow this to happen? I know a couple of friends who have it on their cars, but I wasn't sure if it can be done on a 99 Bonneville SE.

You won't be easily able to do something like that. While the factory keyless entry does as you mention, when the aftermarket unit is installed it simply just triggers the wire attached to the lock switch on your door panel. The Viper unit has provisions to accomidate for priority door locking (read, has an output for pass door unlock that can be programmed on). Unfortunately unless you added an aftermarket actuator to the drivers door, used the standard unlock output on the actuator, then used the second unlock output to the lock switch you don't have a feasible way to accomplish your goal. Newer GM vehicles with databus controlled locks allow for drivers door unlock priority with aftermarket alarms using a special interface module. In your case you just don't have a simple way of doing this.