For the record, I'm aware of seven or eight versions (for lack of a better term) of The Godfather that have seen theatrical service.
A run of around 300 prints were produced by Technicolor in 1972 by the dye transfer method. These were in service for a decade or so, along with other variants.
After GF2 was released, and additional prints were needed, they were produced via auto-select from the OCN at Movielab in Hollywood. This was the first of many situations that placed undue wear and tear on the OCN. Duping stock was not good enough at the time toward the creation of duped printing elements.
More prints were struck at RGB, both from the OCN, re-cut (incorrectly) to A/B rolls, with an additional dissolve added that had never been in the film, along with some dupes.
The final run of pre-restoration prints was struck at deluxe around 1997. Many from the OCN elements, and more via dupes.
All prints produced in 2007 were derived from the restored digital 4k negatives produced via DI.
With the exception of direct positive prints produced for editorial, and a single mute final "density print," which was produced before the final answer print, I'm aware of no other printings.
The separation masters do not match the final cut of the film, as they were produced before the project was locked.
As a side note, there was a set of matrices in service in Europe in 1972, from which overseas dye transfer prints would have been struck, along with various sub-title and foreign track elements. There was also a CRI in foreign service.