Hi Christian, I do some production work on precise pieces as well. To eliminate inconsistencies in the wood blanks, I make my fixtures so that each piece of wood is referenced independently. Here is an example.
This fixture can hold 12 pieces on my 1000x1000. Each piece is referenced to the lower left corner. To make the fixture, I first constructed it as close to square as possible, but each pocket was intentionally undersized slightly. Then I did a final trim with the x-carve to flatten the bottom of each pocket and cut them to the exact size, which makes them perfectly square to my x-carve, as well as knowing the exact position of each pocket relative to machine home. Now I just need to load up the blanks, and reference the carve for each piece to the known location on the fixture.
Hope this helps.