I second Lee's feedback about region rotation, it would be nice to have more control there!
As for the method of using coded targets to align scene, kudos to you James!
Perhaps Agisoft can implement similiar workflow, doing the math automatically? Perhaps it could be as simple as defining that first two markers represent X axis and line from third marker, perpendicular to the line connecting first two, is our y axis?
Maybe we could even place markers at even distance from the scene center (around scanned subject) And have photoscan treat midpoint between markers as the 0, 0, 0 origin?
Lastly, I really wish that manual markers, rulers and coded targets features would trickle down to Standard Edition, leaving all of the advanced ground control, ortophoto and other DEM-related features, plus 4D, to differentiate Proffesional Edition...