...the only thing I can suggest is to fine the most stable ( least amount of change) area on the table that your part or parts fit on and mount/rotate /fit your vise or vises there. If you have larger parts that may not work and the best I could suggest is some creative programming to compensate as best you can. I have at times made fixtures with bends on the face to compensate for parts that stress relieve while machining but that is a completely different issue from yours. I think that was what you boss was thinking of, but as I said they are not the same issue.
Let us know if you come up with a solution... I'm always interested in this sort of thing. Steve