For all the style points on the exterior, I have to take away a ton of brownie point for that interior, and all those $49 each "extras" mentioned should be standard. It looks totally messy and unprofessional, and certainly not worthy of "Premium" or "Reference". You're paying for the brand name, rather than a good system.
And I don't mean from an aesthetics standpoint, either. That GPU is half out of it's PCIe slot, and doesn't seem to be screwed in, from the pics. those cables could have easily have been customized, AT LEAST in length, if not going further by using smaller gauge silicone insulated cables, and maybe custom reduced size ATX connectors to better fit into the case (seeming the reason the GPU is crooked). They could have used a custom SFF or server PSU as well. This just looks lazy.