The SGI machines are geared pretty heavily toward supercomputing applications. As such they're tailored for applications that need to share data between processes efficiently, and that also need to do a lot of computing.
The SeaMicro server probably would look pretty lousy when compared on SGI's turf, since Atom processors aren't designed to be performance-competitive with the current desktop and server processors.
What would make more sense is a comparison a datacenter for a company like Disney or Google or Amazon. I suspect that even though SeaMicro's rig would look pretty bad for heavy number-crunching apps, it would most likely do very well in web and database. Those apps don't need to share a lot of data between threads/processes, and they're generally I/O bound rather than compute bound. With proper caching setups, they're mostly network bound, rather than disk bound also.