From what you describe that seems totally correct to me.
If you perform a
resection than everything is "hanging" via the zenith/horizontal angles and slope distances on your control points. The intersection point of all the rotation axiis of your instrument will be derived from those and afterwards, via the "instrument height", that point below your instrument. That's the reason why only that elevation is changing if you change the instrument height.

In order to change the elevation of all measured points you'd have to change the observations to your control points, or the coordinates of them. Only then the intersection point of all the rotation axiis of your instrument will change.
------------------------------
Ronny Schneider
------------------------------