Ah, I re-read the MC_GearIn documentation and see that it does state the position will be followed if in Positioning Mode. Thank you for the help!
My understanding is that the MC_GearIn is only trying to sync the Master's velocity to the slave velocity. There will always be some error in the syncing of velocities, and therefore your positional error could build over time without correction. The advantage of the MC_GearInPos is that any positional discrepancy build would be automatically handled. Maybe I don't fully understand how the MC_GearIn works?
I would also like to know the answer to this question. I have tried to use the MC_GearInPos to sync the master X to the slave Y, but it does not immediately sync because crossing the MasterStartPosition is required. Also, if anyone has any clever ways of homing a system with dual x-axis like this I would be interested to see an example.