I think that the big usage for out-of-box graphics cards isnt for things like gaming etc, its for massively bulk dataprocessing, CUDA/OpenCL stuff.

(Although two graphics cards built in is already pretty decently powered)

Author here.

I should have made it clear that gaming is the only reason for me to add high end cards.

Is a Mac Pro with some graphic cards really a good choice or would a cheap (read: $300 for the base system + cards) self build Intel / AMD box be a better alternative? If I look at current boards with 4 PCIe x16 slots.

A complete box would likely be cheaper than two or three graphic cards for the Mac and it should be a lot faster (TB vs. PCIe x16)