I've never seen a shark fin antenna on an x runner. Especially on an 05. So my guess is that it's aftermarket so it's hard to say what it was for. Chances are that it has no gps in it and even if it does aftermarket radios usually use proprietary gps connections.
As far as the GPS antenna for your kenwood, they don't even need to be on the outside of the vehicle so just put it in the dash somewhere behind the radio and it will be fine. Just make sure there's no metal above it