The CPUs they're using are Cascade Lake, not Skylake. So I'd add at least about $500 there. You'll also need to add ~$300 for the giant 1400 watt PSU, and at least $500 for the custom cooling solution and case. Most PC cases are really not built that well.

Where did you get that $500 increase? Intel doesn't increase prices between generations, at least not that much. If anything, they could even reduce the price to have a chance to compete with new Threadrippers.

The $500 came from the new chips, plus the motherboard Apple is using is much higher spec than the SuperMicro.

It's got 8 full length PCIe slots, and two of those are the MPX slots so it's effectively 10 if you use MPX cards. It has dual 10gb NICs, and two TB3 ports.