Your thread title should be reversed: "Two cassettes misaligned on Campagnolo derailleur"
The RD is attached to the dropout. If the cassette on each wheel is the same distance from the dropout, & thus the RD, they will shift the same.
The trick is to shim between the freehub body and the back of the cassette so that the small cog is the same distance from the axle locknut (or equivalent) on both wheels.
This can be done with shims cut with knife or scissors from beer cans- about 1mm.