In applications such as the crank and trans bearings, the bearing would be pressed onto the shaft. The most common clearance I've seen are C3 bearings. This allows the bearing to be pressed onto a shaft, and roll without binding. Once the bearing is pressed onto the shaft, that clearance all but disappears. If I feel any up and down play on a crank end installed in a crankcase, the motor comes apart and new bearings go in.
Do as you wish. I only base my comments on 40 years of working on bikes and doing mechanical fabrication, going to factory service schools, and building bikes that won a few national championships.