I've rebuilt one....no maybe two NSR250 engines and I don't think that I've ever paid any attention to any white dots.

Let's have a look at it logically.

The engine doesn't have a balance shaft, so there's nothing to align there. The primary drive gear fits on splines to the crank. there's no missing spline to locate it so it can be fitted in any position. It has no lightening holes, or offset weights so chances are the COG is pretty much in the centre. If exact rotational location was necessary then Honda would have made it fool proof and punched or scribed a permanent mark of some sort.

The primary drive gear drives the primary driven gear on the clutch at a ratio of 2.36:1 (MC21) or 2.5:1 (MC28), so if you align anything statically then after 1 revolution of the crank you're gonna be miles out, so obviously nothing needs aligning there. You can see that the 28 would requires 5 revs of the crank to line up the dots again. The MC21 would align every 59 revolutions.

Other gears attached to the primary are the same story.

The answer is, throw it together and don't worry. If it vibrates then something else is wrong. It's not due to misalignment of the gears .