PSU? What else are you going to run your FPGAs off of? A few dozen <75% efficient chinese wall warts?
HDD? USB stick or CF card in PATA adapter. Even a 7.2k 2.5" is <1W spinning.
Mobo? I give you that, 3.5W vs. 20W peak ...
So we're talking about 430 vs 450W for 10Gh with S6s, 23.3 vs. 22.2 Mh/J ... not exactly a massive deal.
For something with efficiency similar to BFLs vaporboards, it's even less of a difference, 2-3% max.

Now, what something like a pi does have going for it is power (see above, not *that* big of an issue), cost and size. = A lot cheaper, and way easier to tuck into a corner somewhere.

Benefits of a generic x86 ... can install any random OS, way easier to set up a full dev toolchain without having to fiiddle with crosscompiling, > 256MB RAM. Also potentially a lot faster and has GigE (somewhat pointless here...).

So yeah, if I wanted to build a few dozen 10Gh rigs something like the pi as a controller would make sense... for a one-off... too much work, just slap a x86 in.