I guess you are right there. Putting a standard offset in and having the ability to change it might be enough. That would also make it less complicated for the end user as they can just leave the standard instead of having to do more calibration.
The question would of course be: How would we find out which offset we need? I guess if you can get coordinates of both the hmd and the controller, you could calculate their relative position using angles. The rift can even accurately show rotation so that could help too.