Thinking some more about it, if the short block was built, and the pump and shaft was in the block, rotating the assembly over without the distributor in the block wouldn't show contact with the counterweight either by rotating the assembly, and looking for a spot of binding visually, or going by feel for a point of resistance. Only when the distributor is installed and the oil pump shaft is centered would there be contact with the counterweight.
Depending upon how clean the used crankshaft counterweight was when assembled a witness mark could easily not be seen if there was only light contact.
The metal produced from contact would also explain why cylinder walls and main and rod journals might be damaged from a extremely low hour run time, requiring rings and bearings on the second build...….