Never seen a receipt for $25,000 on one computer... but my university comms department did drop 2.5 million on updating the building's labs with 23" ACDs and pretty high end Mac Pros.
Configuring a Mac Pro, then adding 98 more of the same configuration, then adding 99 vTraks isn't a big deal everyone.
The only thing good about buying the parts directly from Apple is that they will be covered under Apple Care, after that, it's nothing else. I still wouldn't buy from Apple but it does have it's advantages for some people.... I guess.
The advantages are debatable given the comparative level/quality of expertise of many AASPs and Apple service itself (well, the fact that it's crap is not debatable), but it's something that as a business it's best to do from a cover standpoint. We've never maxed out a Pro but most of our recent ones have the full complement of SAS drives, RAID and the FX5600. Unless it's external, we don't buy third-party storage or memory.