So for $56k USD you get a system that is roughly twice as fast as the 4x Mac Pro solution... but also costs twice as much? The numbers actually don't work out too badly. At least, better than I would have initially assumed. Density is really the only area where the 4x Mac Pro solution loses hands down.
There's also local storage. The SuperMicro box can host a lot more storage locally than the Mac Pros can do easily (you'd need external Thunderbolt2 drives), and it can make sense to run RAID-10 or something to get more speed.