Hmm- maybe they are for future expansion or to accommodate a different board they were considering?The 2 other connections don't go anywhere on the GPS board, the 3V3 testpoint on the GPS board is just that, a test point for the 3.3v LDO which supplies the u-blox. 5V comes from the Solo, goes to the 3.3V LDO.
On the Solo I can't find any connections to the 2 Mystery wires in the cable (orange & blue)
In the attached photo of the gps connector you can see that the 3V3 testpoint trace goes by the connector and the 5V trace goes to pin 1.
I don't know but thanks for the info!