It's unlikely that this company needs all the hardware features of the Mac Pro - probably just the beefy GPUs. That's combined with the power density problems (and higher monthly costs) of this solution, compared to modern rack or blade servers, making it far worse value.
Compare this also to John Siracusa's woes over buying a new Mac: He wants a graphics card powerful enough to game on, and remain useful for a number of years. He wants to be able to get a retina display. He's for now stuck with a 2007 Mac Pro as Apple don't sell a suitable machine.
When I was comparing hardware, you really couldn't buy comparable cost/flop GPUs for any significant savings (and you'd spend more on some similar builds), which was my point. No idea if that's still true. The idea that you could get the same thing for half the money just wasn't true.
Your comment about John Siracusa's problem doesn't seem relevent to the OP, although it something to consider if you were buying a machine for home use.