Large-format FPGA people won't bother with most commodity hardware in such a manner. They know the value of their time, and want something fast and reliable, so they choose something turnkey like LargeCoin.
By the same logic, Google would also choose something turnkey instead of off the shelf hardware, since they know the value of their time.
The key thing to remember is whether your custom solution is actually cheaper than the off-the-shelf solution. Let's take the example of singles vs. largecoin: LargeCoin is supposed to get 20ghash at 100 watts, in a 1U rack formfactor. BFL singles do ~830mhash at 70 watts (before PSU losses). So, about 25 Singles to each Largecoin. 70x25=1750 watts. Space taken up would be a lot more than 1U, not sure how you would fit it into a rack properly anyway. ~$599x25=$14,975 plus shipping. LargeCoin was (for a brief moment) $15,000, but presumably that is sold out at that price and it will go back to $30,000.
Now, assuming you were a lucky first-25 LC customer at 15 grand, we can compare the 2 solutions based on price. Most anyone has 1U somewhere and 100 watts is just another lightbulb's worth of power and heat. 25 Singles is probably going to take up a bit of square footage, but if you have the space that is cool too. The main killer I think would be the power - sure 1750 watts is the same as a powerful quad 6990 rig with an OC, but it is 17.5x the LC wattage, not to mention associated cooling. If you have free power, BFL is the way to go. It just has drastically reduced scalability.
Now let's say you were too late, and LC is going to cost you the full 30k. If you have free power and lots of space, BFL is certainly the winner. You could even develop a watercooling system just for them. But if you want to put them in a datacenter, I'd say that 25 would probably take up 6 to 8 U for a bunch on a shelf with some fans for cooling, and a 1U atom-based rig to run them. Calculations based on 19x29 inch rack and BFL measurements of about 4.5 inches cubed plus space for air and wires (15 per 4u shelf). Since power and space are the primary cost of any datacenter, LC starts looking better (although still not very competitive).
The only other main point is reliability. Where there are more parts, or more moving parts, or more anything, there is more to fail and go wrong. LC being a single solid-state appliance with presumably just a few fans would likely be less hassle than 25 units with 3 fans each, statistically speaking.