If I understand correctly what a separation master is, it is the film copied to three separate monochrome (black and white) copies each of which represents a colour (R,G,B). So while it is a perfect colour-timing reference because it shows the levels of each colour separately and doesn't fade, it would be a really bad source for scanning the film as it would mean doing everything that is normally done for a film preservation three times and then you'd have to align the three separate scans => three (maybe four) times the cost of a normal release.