Dana 60 gear

Do you have a picture of the pattern? There is the chance of operator error when the gears are lapped in together and the determination of pinion depth is made, as it's made on the determination of blueprint dimensions. They are more of a guideline to help get you reasonably close (especially on a used gear set!). There is also some allowance for machining error in the center section of the axle. As long as the bearing races are fully seated in the housing, pattern and preload are king. It looks like you know if the measurements don't match the numbers, the gear set will care a lot less than if the pattern, preload, and backlash aren't properly set. But to answer the question, it's not uncommon to find that the numbers are out to lunch, and I'm sure that some brands of gears (or certain series numbers of axle housings) are worse than others. If it were me and I didn't 100% like the pattern, I would work with it until I felt confident with what I see.