I tried using a redundant installation, like this:
- Genesis: F:\Emulators\NeoGenesis_v24\Genesis\default.xbe
- Sega CD: F:\Emulators\NeoGenesis_v24\SegaCD\default.xbe
- Sega 32x: F:\Emulators\NeoGenesis_v24\Sega32x\default.xbe
Unfortunately, when I tried this configuration I was surprised at what actually happened: each time I would change the "media directory" settings for one it would change the settings for the others. In other words, I would set the Genesis directories to the Genesis media folders (F:\Media\Genesis), and it would alter the SegaCD and Sega32x as well (F:\Media\Genesis). Furthermore, anytime I changed the skin for one it would change it in the others as well. Weird....
Obviously the directory-structure is only part of the problem; they must be connected in some other way, though I'm not sure how or where. This issue appears to be consistent with XboyAdvance 23 as well (as I'm trying to achieve a similar configuration).
PS. I quadruple-checked my EVOX.ini path settings to make sure that wasn't the problem, and it isn't. All emulators are pointing to the correct directory, so that's not the problem.