I hone the inside of every pinion bearing when I build a rear end. You only remove .0005, then it still knocks off and on, not a slip fit. This let's you use the same bearing you set it up with.
I also measure the case offset of the carrier bearings so I know what to compensate when measuring off the cap pads for pinion depth. But I have depth mic's, gauge blocks, test indicators and a surface plate. Lol