You do realize that they can heal 1.1k MP only during trans and only once, since it has a cooldown...making that scenario happen once every 36 minutes, not 3? In other words, it is 12 times not as bad as you're saying it is.
You realize Transformations can be extended via rebirths and aging to 10 right? I'm pretty sure there's lots of Falcons that lasts over 10 minutes.
Also Dark Knights trans last really long if they can outheal their drain. The max MP they can get is 2.1k MP, allowing them to heal 1,050 MP. That's still a lot.