This is a very interesting development!
Maybe, I might make a suggestion or two: conf.ini settings in the [Mods] section have very technical (per se) looking names, and the range of inputs which can be used for them, and which input is default, is not always clear. Sometimes, the effect is not always clear too: for instance, the SpeedbarTAS setting could change the displayed speed to TAS, or add TAS as a second displayed speed, but it is not clear to someone who does not already know. The same lack of clarity found in these simple setting names can be said for, in some cases, which setting is used by which mod.
My suggestion is this: define and include a file—something like i18n/mods.properties—which controls the names of the properties as seen in this menu. For instance, "ReticleBrightness" might change to "[Reticle Brightness Config] Reticle Brightness (defaults to 70)" and "ngMAPhostile" might change to "[NG-MAP v3.1] Enemies on Map by Default (defaults to 0)".
Restrictions might also be implemented for certain settings like ReticleOnAtMissionStart so that the user can't set it to, say, -3, which may have disastrous or strange consequences. Maybe, certain settings could be marked as the "0=no 1=yes" type of on-off setting, and the "Value" box for those settings might be, instead of a text entry box, a dropdown menu with the options "False" and "True".
Anyhow, I feel slightly rude by now, having dumped all my ideas on you, but I hope I've given you some ideas if you weren't considering anything like this yet. I really like this development, and I'll be waiting for v2.1 with baited breath.
Cheers, and happy modding!