In OVGME, during Make-Mod Archive creation, you already must create a section for mod description and mod version numbering: add a checkbox in Make-Mod window for use Main dir or Saved Games Dir, this value will be saved in the txt file zipped in the archive of the mod.
Actually my mods published here are only OvGME compatible, I don't see any difficult in a config file done using an interface. I'm with you when you say you want mantain an universal app for mantaining mods, but you are posting in DCS forums: if you make a poll here, you can imagine that every people want a DCS oriented app:music_whistling:
If I was capable, I would already downloaded the sourcecode of your OvGME from github and started working on it: sadly, I'm not a programmer;)