Well, for me the solution was to delete the extra bones since they were not needed in my case. Also the extra bones were greyed out since there was no skin weight painted on them (not sure but I think this in part was responsible for “set master pose” to go crazy).
So I would suggest to have the extra bones that you need at the end of the hierarchy since the problem might be related to the bone order and to make sure you have skinned these bones.
If this does not help I would guess the only way would be to have these extra bones on your original skeleton as well.
Good luck!