Apple's web store shows the basic dual 2.0 Xserve G5 cluster node for $2,999 in unit quantities.
The rest of the $5.8M is probably for ear protectors :-) If you have heard the sound even a single Xserve makes, you'll know what I mean.
Seriously, the leftover $625/unit is probably for RAM. The ECC RAM runs about $240 per GB in unit quantities at memoryx (you can shove up to 8GB into each of the G5 nodes). I suspect someone like Colsa is not spending the money to cram extra hard drives and optical drives into each of their nodes.
- kc