XPort, as Hargle pointed out in the Screenshots thread, wouldn't having 2 copies of the emulator make for configuration overlaps as well? As the emulator (regardless of how its renamed or how many times its copied) is still going to reference to e:\UDATA\{somehexnumber} for their configs. So if you set one version of Mekax to save in one location, it would ultimately overwrite the settings for the other copy of Mekax.
I hadn't put much thought into it previously, but people using Relax/Samba shares are also going to be heavily affected by this. Those people don't want to rename their master sets that they've compiled, as they might be used in other emulators/applications as well. I'm seeing now that it isn't just a SMS/GG issue, but also includes Sega CD & Sega Genesis as well (since many of the Sega CD releases were upgraded Genesis games like Earthworm Jim, Mortal Kombat & Ecco). With the rekindling of Sega CD interest (thanks to you're updated NeoGenesis) most people are going to be playing the games off of the original cd, a dvd complilation, or streaming them. You can't quite just rename a game on a cd/dvd, so those users will just be SOL unless they go burn another renamed set.
I don't want to come off as sounding demanding or arrogant, but I feel this is a larger issue than most people know. Most people probably haven't paid much attention to their screenshots as it is a lot of work to make a complete collection, or because Chron Johnson and myself have provided packs to them. People might also not realize the reason their save games have suddenly become "corrupt" due to one system overwriting it with another, and the emulator not being able to load a save state for a different type of rom. If implementing this is too complex for one reason or another, I would be pleased with some alternative work around. Anything other than renaming the files, as that is not an option in many cases. Thanks