Tom,
I think you answered your own question in post 1, but I,m guessing when you mention the rear base, is this one of the PH ones that flips up ? I,ve used them in the past with downloads and sub Calibre kits etc, the rear base always seemed to be off by a mile, sometimes (depending on what type of scope rings) could be adjusted by turning the rings around.
As its 0.060" it won't take much to shim it and if the whole scope is offset by 0.060" I,d leave it as it is.