Just some food for thought. After playing with FSX for a while I think this issue is more a matter of a game supporting 6DOF.
In FSX you can zoom in with the - and = keys, giving you a high degree of magnification. Then using the Trackir you can zoom in on a smaller scale in your cockpit. Therefore there is no need to have a separate center adjustment in the Trackir software as you can zoom with the - and = to set your center then zoom separately with the Trackir.
In a game like Lockon however, there is only one zoom. There is no separate high magnification zoom with the keys and a smaller scale zoom in the pit with Trackir. Therefore to zoom in Lockon with the Trackir you are simply moving your head on the z-axis too much to go the full range. I actually turned off the Trackir z-axis because of this and am using the keyboard instead.