In a modern manual transmission ALL the gears are meshed all the time
Diagram here:
https://s.hswstatic.com/gif/transmission-5speed-gears.gif
Green shaft spins at engine RPMs, it spins the red shaft that has "the gears", which spins the Blue "gears" even Reverse
In the drawing the transmission is in Neutral
The three Purple "dog gears" are always connected to the Yellow output shaft
The shifter moves the dog gears to engage say 1st gear, the dog gears are where "syncro-mesh" is used, as the dog gear slides into 1st gear the syncro slows down or speed up 1st gear to match the RPM of the dog gear
The clutch disengages engine RPMs which allows 1st gear to speed up or slow down, to match dog gear RPMs, which might be 0 RPMs if vehicle is stopped.
So gears spin at Engine RPMs only, even in Neutral
The dog gears and output shaft spin at vehicle speed RPMs, drive shaft RPMs
So it REVing the engine changes "whining" sound then its caused by input shaft or gears.
If SPEED changes the whining sound then its output shaft related
Yes, it could be the Mesh on one gear that's making most of the noise, so when using that gear noise would change
Helical gears(angle cut) are quieter than straight cut, but helical gears also put forward and backward thrust on the shafts, so stronger thrust bearings and trans cases are needed