OEM built machines are often better than home-built counterparts, predominantly because OEMs understand how to balance all the various components to get better overall performance. 64-bit probably helps a bit, but not usually by a significant amount.
If someone's doing a "home built" it means they're after components that are more suited to their requirements; there really don't exist many bottlenecks and in my experience OEMs deliver worse performance/currency than DIY boxes because they build for the
80% case which doesn't need "overall performance": they're engineered to reduce support costs and keep manufacturing costs down. I may remind you that many OEMs were guilty of still using Intels not-good-enough-for-Vista IGP chipsets well into 2008 whereas
everyone who builds their own were using cheap 'n' cheerful (yet in comparison, blazingly fast) entry-level GeForce cards.
Right now I'm using a box I built by myself, Q9450 with a GTX280 that cost me significantly less than a lesser machine had I bought it from any of the major OEMs (or even Alienware).