CPU: Xeon E5-2697 12-core 2.7 Ghz - $2749.99
Video: AMD FirePro S9000 6GB - $2199.99 ea. (close as I could get) - x2 $4,399.98
RAM: G.SKILL Ripjaws Z Series 64GB (8 x 8GB) 240-Pin DDR3 SDRAM DDR3 1600 (PC3 12800) Desktop Memory Model F3-12800CL10Q2-64GBZL - $599.99
SSD: SAMSUNG 840 EVO MZ-7TE1T0BW 2.5" 1TB SATA III MLC Internal Solid State Drive (SSD) $569.99
Motherboards that handle 64GB of RAM look to be generally under $400
Let's add $300 for case, PSU etc. and we're looking at ~$9000.
So even if the individual upgrades are badly priced (64GB of RAM for $800!), the entire system is actually pretty fairly priced at the top configuration. The tight integration of the parts, and I'm guessing sourcing directly from the manufacturers rather than through 3rd party parts builders, probably cuts lots of the BOM out. And there's no way Apple won't make a profit on these ugly things.