Apple is still charging a hefty premium for CPU and memory upgrades, so the lower-spec Mac Pro’s are still likely cheaper than DIY builds. It appears that the reason for the price differential is that AMD is giving them a screaming deal on the video cards: for the top-line cards it seems that “AMD is allowing its $3,200 workstation card be sold on Apple’s latest Mac Pro for about $750. That is the number one reason the PC loses out in this particular battle.”
You probably save more (as compared to DIY) as you upgrade the video card, with the savings more than offsetting the DIY losses when you upgrade the CPU and memory.
