You could have 100 of the exact same engines running the exact same route on the exact same fuel, all on the same day, and have 100 different MPG numbers. Just small differences in machining can and will make a big difference.

The biggest differences would be between the last engine cut on tooling at the very end of its life, vs. the 1st engine cut on fresh tooling. Big power differences between those two as well if you were to put them on a dyno. This is why custom tunes are always MUCH better than buying a canned tune that works on every vehicle. It'll be close, but those minor differences between the same engine come into play.