The major difference is that the Type XII's are available to Size 5 ships, while Size XI's are only available to Size 7 ships (or larger). That's certainly worth an extra space.
Also, with the abstract system that is the ship construction rules, you can't limit yourself to thinking with only the points in mind. Forget what you have learned with the FASA Tactical Simulator, Starfleet Battles and Spacedock, and start thinking with a roleplaying mind, because this system is designed to complement the RPG (and not act as a stand alone combat simulator).
Type XII's represent the latest in Starfleet phaser technology, so it would be natural for the fleet's newest ships (those that can fit them on) to carry the best technology available. That fits the concept of the Sovereign. No, the greater capabilities of the Type XII may not be readily apparent within the limited scope of the abstract design system, but if you think in Starfleet terms, they are clearly the better weapon.
To be honest, if you want to completely munchkinize the Sovereign, why stop at just using Type XI's? Save 14 points and go with 22 Type III phasers. It gives you the exact same OV, and you have points to make the ship as uber as you want. Maybe you could take those 22 points and add three more Mk 95, and still have enough points to add another tractor beam or your super-secret uber 50OV weapon that ignores shields and costs 1 space.
You can see how quickly this can become ridiculous...
Davy Jones
"Frightened? My dear, you are looking at a man who has laughed in the face of death, sneered at doom, and chuckled at catastrophe! I was petrified."
-- The Wizard of Oz