I suspect it is subtle changes in the amount of backlash in the gear mesh. My Ducati has helical cut bevel gears that were lapped at the factory and have to be shimmed to the same minimum clearance as they were set up to at the factory.
It costs money to lap in and shim precisely gears.
Gears whine because the gear faces are hitting each other taking up the clearance differently as the gear rotates. Round is not always perfectly round. If the clearance is less, and you are lucky with nicely matched gears, then the box will be quieter, but still whine. Too much clearance and you get clatter on neutral throttle which is the noise of the gear faces slapping against each other on each side.
Straight cut gears hit across the whole straight width of the gear providing a wide contact line that does its best to roll around the involute form of the gear surface, whilst helical cut gears slide against each other along the length of the gear; so its a softer transition of forces. Hence less noise, but weaker gears.
