Is it common practice to drive a ground rod and bond it to the case for a stand-by generator? It depends on your next question.

Does it matter if the generator is considered a seperately derived system? Yes
If it is a SDS then the neutral and frame are bonded and a ground rod is installed and bonded to the frame.

For it to qualify as seperately derived the neutral has to be switched in the transfer along with the ungrounded conductors right?
That is correct

If my understanding is correct, since this isn't considered a seperately derived system because the neutral isn't swiched shouldn't this neutral bar be isolated from the ground? Yes

If the neutral is NOT switched the system neutral is connected directly to the generator neutral treminal.

The system EGC is connected to the generator frame and remove the bonding jumper from neutral to frame. You may install a ground rod and bond it to the gen frame. It is not required.