I think that bounding box should be optionally liked to ground coordinate system once that absolute orientation is done by means of GCP. Height-field would then be exactly calculated.
My suggestion is to allow user to choose this behavior and also to lock bounding box rotations around x and y so that "gravity" direction kept aligned to z axis ruling the mesh creation as does in the actual terrain modeling. (the third rotation and re-sizing should be kept up to user).
regards and congratulations for last improvements.
JMR