5% on a 600 HP engine is 30 HP. So are we talking a 60 HP variance (which I think is too wide)? If so, I guess you could even live with that much variance.
You points about how the parts are machined is correct, but again, as an engineer, you know when things are designed, there is a +/- factor built in. Possibly the engineer left those things too wide open. Anything is possible.

But I can tell you that I just don't see how there can be the wide variation of numbers, unless there is a lie, or the dyno (or flow bench) was made as cheap as possible.