The XC only feels higher because KTM shaved the seat on the SX models to achieve a lower center of gravity (with the rider mounted that is) and to allow better movement around the seat in corners and such. Either way, I feel the KTM's are far more comfortable than LTR's and feel more like a Honda where you are a part of the quad, and not just sitting on top of it.
Honestly, be serious with yourself and what you will be using the quad for. I agree, the SX looks a little meaner (mostly due to the hood in my opinion) but looks don't mean a whole lot. The SX is a purpose-built MX'er that should only be used on the track, maybe with some dunes as well. Trust me from experience, it does not like being on trails. The engine is too rev-happy and doesn't like holding gears. It wants to be revved quick, shifted, ridden hard, etc. These are not ideal characteristics of a trail quad or GNCC/XC racer. I raced my SX in a Grand Prix race a couple of weeks back (half MX, half desert) and beat the crap out of myself. If you plan on trail riding, racing desert, or whatever, the suspension and engine on the XC is far more appropriate. Torque and a more plush setup are what you want here. I think the XC would make a better duner as well since you could run it a gear high and still have the power to pull a hill. Plus, for the ~$3k you'd be saving, you could do some engine work and have a real hill shooter or trail monster, and have some money leftover to revalve the shocks (if need be) and put SX a-arms on it.