Just had the Mopar remote start installed on our 2010 automatic. I believe the "bypass" your refering to may be needed if you have the "Sentry" security key fobs. These fobs have a computer chip in them that if not present when the Jeep is started, will only run the engine for a few seconds then shut off.
When I picked up our Jeep at the dealer, the new remote start did just that...start, then shut off after 15-20 seconds
They reflashed it again and it still did the same thing. I said let me take it it home and I'll see if it continues to malfunction
On the way home I had a hunch that it may have something to do with the Sentry keys. I removed
the OLD key fob and new spare Remote start key fob from the vehicle and presto... the remote start functioned properly. For some reason it appears that having the OLD key fobs present with the new "remote start" key fobs confuses the Sentry security system