With the way Honda set up the alarm, if the alarm is going off and the battery is disconnected in an attempt to shut the alarm off, it will trigger the alarm to go off again once the battery is reconnected. This maybe why the alarm is going off when he connects a battery to try and jumpstart it.

If the battery was dissconnected/dead for an extended period of time, it may have reset the alarm to the point that it may not recognize the code from the key fob transmitter. This could by why the remote does not turn the alarm off.

Thus, the only way to disarm the alarm is to put the key into the ignition and turn it to the on position.
Catch my drift?