520T & a drained main battery

So, what is suppose to be the disarm sequence after the 520T triggers an alarm due to the battery being disconnected or in my case, the wife leaves a door ajar and the interior lights drain the battery to a voltage level that triggers the 520T? The passive arming and forced arming was active, so the alarm bypassed the "door ajar" pin and was armed passively.

When the alarm triggered, no matter what I did, the remote wouldn't disarm the brain and I had to get under the dash and pull the plug on the 520T. Shouldn't I have been able to disarm the brain with the remote since it was powered? Also after I charged the main battery, I had to go through some funky remote button pushing/valet button pushing/ignition key on/off sequences to finally set the alarm "back to normal".

Thanks, Steve