None of these aftermarket units, including the EC Offroad interface module I'm currently using, Naviplus, Grom, etc. seem to attempt to use the factory GPS antenna, which presumably must plug into the factory head unit on one of the connectors. I've wondered if there's a good reason these always come with a plug in GPS antenna - could be that the factory GPS antenna is difficult to adapt for some reason.
IIRC, at least some of the aftermarket units do make use of the factory mic. The unit being discussed in this thread does have a built-in mic, so I'm wondering if that might work well enough.
I would definitely be interested in using the factory mic and/or GPS, but not if it means making changes (cutting wires) that would prevent reverting to the factory head unit at some point (just in case...).