I have a couple customers with the Custom Axis rear. Axis goes with a single rate due to the linkage leverage ratios. They say it performs better.
Now as for the ride height, you will have more adjustment with a aftermarket rear and will be able to get your ride height down. The key though is to get the sag ratios correct. You will have to switch to a "zero preload" set-up to drop the quad to a great degree.
thats what I was afraid of. I got the GT Thunder revalves and linkage, but the seat height seems just as high as stock. It rides a whole lot better, just want to get the rear down another 2 to 3 inches to get it more stable.