I'll freely admit that I've been assuming a particular set of things:
1) That the lift crystal is the big one because that's the one that deals with the biggest force: gravity. It makes structural sense to have a single large one at the center of gravity; it's easiest to design a support system that hinges on one point of force instead of multiple. Having multiple smaller lift crystals distributed throughout the ship would supply a lot of redundancy, true, but it would also make designing supports far more complex and make managing their output perhaps beyond the capacity of a single pilot. It's the way I would do it, anyway. May also have something to do with the higher efficiency/effectiveness of a single large crystal as compared to those of multiple small crystals.
2) That the attitude crystals can't be set to provide force along varying vectors, not just with or against gravity. I've personally seen no reason to think that something that applies a force must be limited to one axis (again, I may easily be wrong on this, so grain of salt, etc.), and with the lift crystal's support system supplying a central axis point, it would therefore be easy to distribute attitude crystals to work around that rotational point in all three dimensions. (Again, see maneuvering thrusters on, for example, Apollo spacecraft.)
A lot of assumptions, I know. But they make engineering sense to my eye.