The other thing to consider, Jeff, is the quality of the throttle body. I would not be surprised to learn that a 54mm HPI throttle body outflowed a stock HD 58mm throttle body. You made a good choice by sending your HD throttle body to HPI for modification... 
That's an apples and oranges comparison. HPI does not make a 54mm TBW TB. (yet)
I think maybe you mean Jeff's stock throttle body modified by HPI to 54mm will probably out flow a
stock HD 58mm TBW TB.
That I would agree with after looking at the roughness of my HD58mm TBW TB.
Just note that Jeff's HD58mm TBW TB was modified by Cycle Rama so it can't be called stock either.
How about this, send a stock 50mm TBW TB and a stock 58mm TBW TB both to HPI, and then check the flow, that would be the telling difference there.
Then it would get back to the makeup and the ability of the engine components to handle the flow delivered by either of the two HPI modified TB's.
It's what I have learned from this site many years ago.
It's not the value of each individual component, it's the sum of of the combination that produces the best package.
SBB