It's not the "configuring" that takes time, it's merging the data. You need to snapshot the old servers after they come down (which likely takes hours), transfer the data to the new ones, (likely hours more, given how much there is), and then merge all the data back together again, likely one by one to make sure you don't have collisions in names, etc.
Then you have to run through the entire combined set again for verification, comparing the result with the two original sums to make sure you aren't missing anything, probably wipe a bunch of caches, and only then bring things up. The last thing you want is to come back up from the merge and have Little Johnny putting in GM pages saying he lost his Excalibur.
If at any point you notice a discrepancy, you have to stop the presses and start over. And you have to do this for each server you're merging. 12 hours is actually pretty impressive, considering.
Edit: It also amuses me that people blow off the 12 (15 now?) hours thing as a major inconvenience, but would likely *** loudly if someone told them to randomly work a 15 hour day with no additional pay or overtime. There are plenty of things to be pissed off at SE for, guys. Let's give 'em a pass on this one.