FWIW, I like to set the bore gauge up to read the “clearance”.
I set the bore gauge to zero from the measured shaft diameter.
Install the bearings in the mains, TQ to spec, and check the ID with the bore gauge…….read the clearance.
If the crank measures big, there’s no reason to believe the clearance wouldn’t be small.
Personally, I have no problems running bearing clearances that are at the max clearance spec, or more.
But I’d never put something together for an application like you’re building with clearances tighter than .0020………and I wouldn’t feel all warm and fuzzy about that clearance either.
Imo, you’re looking for a crank, or someone who’s real good with a crank grinder.
If the clearance ended up at .0035-.0040”…..I wouldn’t even raise an eyebrow.