I have had quite a few engines that would suddenly drop one qt at 3000 miles. I would then change the oil, filter, and go another 3000 miles. I do not actually consider that all that unusual. I have had quite a few new engines do similiar things.
Is there another reason you might be questioning the rebuild? It might be me, but I consider 3000 miles time for a change anyway. That has always been my way. My new 383/350 does the same thing. 3000 miles, down about one qt. I feel pretty comfortable with that.
The vaccum leaks I had to chase are another story. Sloppy fittings, line ends, warped carb base. The oil was quite in line withe what I consider "normal".