you can run it down the driveshaft, but its a bigger pain to install and there will also be a small bump where the wires are. If you have a lot of people in the back seat over time it could get stepped on and eventually the wires could fray.
And it could go over the passenger door as well, but its easier to remove the drivers side dash than the glovbox, plus the wires would have to go under the trim holding up the headliner, and on an older car its usually not a good idea to start messing with anything near the headliner for risk of it coming loose.
As for whine, I have it now due to a bad ground, but I did not before I changed the HU even though the subs and evertyhing else predated ny HU, and my wires in run in the manner I described. You shouldn't have to worry about it as long as you have a good ground.
<span style='color:gray'><span style='font-family:Courier'>1995 e36 3 Series RIP
1999 e46 3 Series BURN IN HELL
2000 MR-S Roadster= Current</span></span>