Looks like it starts at only $500 more than the desktop version but I didn't bother comparing specs. I have a friend with a 192GB new Mac Pro he's using for video production and he's currently testing it and finds it outperforms his HP Z8, he's very happy so far.
It actually has a slower CPU, and fewer of them, according to him. But these kinds of machines are where GPUs, architecture, and software all come into play. Cores, bus speeds, subsystem speeds.
There's vastly more to computer performance than the reductionist "It's a PC, in a nice, expensive machined case". In fact, that sounds condescending and dismissive rather than a comment in search of enlightenment.
But all of those things you've enumerated are available in a PC - Apple only makes the board and a few smaller unimportant chips that don't affect performance. You're not comparing apples to oranges when you say that MacPro is faster somehow. It'd run at identical speed given the same CPU, same GPU and same RAM.
There might be benefit from some of the extra bits available (the specific GPU in Mac Pro is not exactly easy to replicate elsewhere as it's a custom twin GPU setup with extra bus for cooperation with another unit if necessary) + the FPGA codec card that might be exploited by the stuff he does for work.
Replacing a software-only codec with hw accelerator card would go a long way to explain performance difference.
Sure, if you're a creative professional or Mac developer you are probably making at a minimum 20x the cost of this box. If you're in an office a rack mount helps save a lot of desk space, which more than pays for itself. Also lets you get away from the sound.