SRT,
The way I do the z offsets,(and this is not to say it's the only way or even the proper way), Is to use a know feature on the Rotary table or the fixture, and incorperate that feature into my drawing. Then if that fixure is used for more than one part or if the part is a "family" of parts then I have something to tie every thing to.
If you use the centerline of the table, in Y, and some feature say the fixture face or even the face of the table platter, for X. Then you could use the centerline of the table in Z. Then you create your model at a known location, in relation to those above.
I don't quite understand why you want to use different Z offsets for each side , but I don't have your part in my hand.
You do know that on a Haas control you can change your Z offset with G10 inside the program? This is handy to "tweek" in only one part of the program.
All the features on your part
WILL rotate around the centerline of your table. So if you use that as your c/l of your model then you will always be "in sync".
As always if I am missing something "SET" me staight, if your think you can.