For Tekkit the config files would be in the %appdata%\.techniclauncher\tekkit\config but you also have Redpower, EE, Buildcraft and wireless redstone in the \.techniclauncher\tekkit dir and not config. This is why I had said it *COULD* be an issue, but I believe the config files are universal locations whether it be server or client, and they are named the same. So I was thinking it could be possible to just require the user to mod say a config.ini for the web-auction to point to configuration files so its less user interaction
Another idea I just had while typing this is how about dumping an ID list right from NEI of all used and unused IDs, this could work as a general full list of whats installed. Format looks like this:
Block. Name: tile.stone. ID: 1
Block. Name: tile.grass. ID: 2
Block. Name: tile.dirt. ID: 3
Block. Name: tile.stonebrick. ID: 4