Aiming
The adjustment between the two optical axes, the telescope and the tracker, may differ. The difference will make it seem like the instrument does not point towards the center of the prism, when using Autolock. This is not a problem since the two axis have their own separate collimation data. It is however important to make collimation test for both axes.
Difference between aiming manually, and Autolock
How to check aiming
You can check how well the instrument is calibrated by measuring toward the prism with and without
If the difference between the read out angles is significant, you should carry out both a horizontal and vertical angle collimation adjustment, and a tracker collimation adjustment.
After a full tracker collimation, the pointing of the instrument can still be different between manual and tracker assisted pointing. The angles to the target in both cases will however be the same - the collimation errors stored for the tracker will effectively make the instruments tracker pointing match the pointing when done with the human eye.