Alan,
from the Epson spec sheet:
Technology
Scanner Type Flatbed Scanner
Optical Resolution 6,400 DPI (Horizontal x Vertical)
Dual Lens System - scanning resolutions Super Resolution Lens 6,400x 9,600 DPI, High Resolution Lens 4,800x 9,600 DPI
If you are using the Super Resolution Lens - 6400 is the optical
If you are using the High Resolution lens - 4800 is the optical.
so depending on the lens used, you would change settings for the scan to retain the most available "real" data.
If the sensor head actually has 6400 sensels, then the scan is limited by the optics and you would adjust accordingly. Epson would be oversampling the High resolution lens path and then reducing the resolution either in driver software or more likely the scanner firmware. It is possible the sensor sensel arrangement is such that can get native 4800, but i don't know.
Using the High resolution lens at 2400 is just keeping every other sensel value and throwing the other one away. Using the Super resolution at 2400 would require down sampling and interpolation, not always desirable, but may not have any practical effect.
If the medium being sampled does not have enough resolution, then both cases would be oversampling. Oversampling can be a good thing if you can tolerate the file size. This, i think, would likely be true for prints. Transparencies, maybe not, but depends on the film and the camera optics.