I think it's largely b/c these batteries are conservatively rated. Figure they might sit in a store room for several months and also must make it to the end of the warranty period still able to crank a motor over.
Plus, I kinda wonder if your tester wasn't calibrated a little off, those CCA numbers can be all over the place with just small errors in calibration. Was it a high quality professionally calibrated carbon pile tester or one of the new pulse types? Were you also able to test any other batteries to confirm the calibration of the tester?
I do know a big advantage of the AGM type batteries is their ability to deliver a large jolt for a longer period than the flooded cells typically can, and they also can be charged at a faster rate.
And I think it's not necessarily a bad thing if the seadoo doesn't top charge the AGM, that's a better alternative as opposed to grossly overcharging and forcing one to vent. Figure you're going to give it an occasional topping charge anyway, so you should be good to go IMO.