I thought it was the other way around. Every MTX 2gnt I've owned had the smaller 49mm TB. Haven't owned an ATX. My brother is huge into neons and the ATX DOHC neons had the 52mm TB's. It shouldn't mess anything up, just a little more get up and go. I think the whole reason the ATX ones had a bigger throttle body was because they were slower to accelerate so they gave them a bump with the 52mm.

And I know first hand that a DOHC neon TB will swap onto a 420a Intake manifold.