Can I use a MPPT Solar Controller to charge my auxillary 12V AGM Battery from the car battery/alternator?
Your alternator is already set up to charge a battery.  It won't put out more than 13 - 14 volts and i believe charge controllers are set up to run form much higher solar panel voltages at much lower currents.   You could just (Jump) the AGM battery in parallel and the alternator would charge it along with your car battery.  You may be over complicating this problem with the charge controller?