The TJ charging system was designed to charge lead acid batteries. The charge voltage is set for that battery chemistry. The temperature sensor (if equipment) is set to raise that charge voltage to assist lead acid batteries in the cold.
Couple of work arounds for running AGMs...add a 40k Ohm resistor in place of the temp sensor which gets charge voltage to 13.8 - still not enough but closer.
Run two batteries...lead acid and a second AGM with a DC to DC charger that's built to deliver the higher 14 to 14.8 charge voltage.
HP Tuners...use it to change the charge voltage range in the PCM.
And I suppose you could interrupt the PCM charge circuitry and replace it with an adjustable external regulator - but I dismiss this option as overly complicated and as expensive as the HP Tuners option.
And honestly these days if you can find a decent battery then run it, chemistry be damned.
-Mac