Usually, the reason people have problems with the Z axis, is from trying to get a lot of travel, as well as a lot of clearance. The farther down the Z-axis is hanging, the more flex you're going to have. There's just no way around it. Raising the gantry up and down wouldnt help much, because you still have to balance travel with clearance under the gantry. And you'd ass a lot of complexity, and the possibility of actually adding more flex.
The easiest solution is to build the gantry as low as you can, with as little travel as you can get away with. That gives you a better chance of getting a more rigid assembly.
Btw, the gantry axis is usually the Y, not the X.