See my comments on your other thread.
The problem with your thought above is what happens if the player changes their mind and suddenly wants to install that wackydo mod that they didn't select when the installer first ran? How will they get that mod "out of the installer and into JSGME", short of totally reinstalling?
In the GW1.1a installer (not the same as the GWX one I referenced in my other post), the installer was done similar to this, with the difference being that the installer took on the role of JSGME. If one wanted to install an optional mod, they'd select it at installation. If they subsequently changed their mind, they'd re-run the installer and deselect it (or vice versa). A bit of a PITA and some users found it confusing being presented with a long list of mods to choose from at installation time, that is, *before* they'd had a chance to read the manual (ie "what's this mod do??" followed by a later "wish I hadn't installed that one"), hence why it wasn't done this way with GWX. I found it much easier to install everything into the MODS folder, giving the player a brief rundown in the installer and pointing them to the manual for more information. *Then* they can enable after they know what it is they are enabling (or delete altogether if they want to)!