The reason reverse gear sounds different for manual transmissions is they are usually straight tooth gears vs the helical gears for all other forward speeds. This kind of gear is what I would expect on an aircraft hydraulic gear pumps or hydraulic gear motors. The reduction drives in the engines are most likely helical as that allows lower collision forces as the teeth come into contact, lower contact stresses, and longer life. Straight tooth gears see higher contact loads but lower bending loads, but used as reverse speed they are cheaper, run at low speeds, and very limited use, so an OK application.
In pumps and motors straight teeth are submersed and cushioned in hydraulic fluid.
I can't say this is the cause of the concerning noise, but as you noted sounds from the Y elec pump, that would be the likely cause there.
Failing bearings tend to squeal or growl rather than hum.