(This item pertains to the check boxes on the General tab of the Setup Options dialog box. You can open it through the F5 key or through the Edit | Preferences | Setup menu option.)
The Force Part Alignment in Car Body check box forces your alignment to be in car body alignment. If you select this check box, no matter what alignment method you choose, the alignment will always match that of the CAD. Selecting this check box acts as a secondary transformation after the initial alignment.
For example, if you translate to the center hole on the Hexagon test block and select this check box, the origin will still be in the corner, but when you report on that hole, it will be perfect since you used it to set your origin.
Alignment before using this check box
Alignment after using this check box