There's distance and there's distance. In the land where you have 48 faders for 48 channels, the distance between channels 1 and 48 can be as much as six feet (analog) plus the time to get there. Boards with multiple layers have less physical distance, that being replaced by the "distance" of time required to push a button.
Pick your poison.
Sure, but with a 48 channel console I would keep the channels I use most often closest to me, and then put channels like stereo returns and such farther away because I don't need to adjust them as often. I can pretty easily reach something 3 or 4 feet away.
One problem I run into with layers is needing to adjust something on one layer as well as something on another layer at the same time. With an analog console the only problem with that might be the reach, whereas with layers I cannot actually adjust two channels on adjacent layers at the same time without doing one of two things:
1. Assign the two things I need to adjust to a DCA or pair of DCAs.
2. Have the channel on the first layer selected and adjust the level on screen and then move to the second layer and adjust the other channel with my other hand.
I've made use of the second method a few times but my preference is to simply setup my user layer so that both of those channels are on the same layer.