This is true. With the analog technology, no two prints looked the same - so taking a few low fade prints as a reference and making a sort of amalgamation of that would give you something approaching the "original" colors. So, I don't think it would be a good idea for a major professional restoration to stick religiously to one particular print, if they have access to more and they probably should keep the clors somewhat consistent throughout the film. What I think should however definitely be done, is to keep the over-all color schemes of each sequence as they appear on the original prints - it would be very wrong for a restoration to attempt to make the film look modern.

The Godfather restoration is a great example of that - the colors are nice and consistent and probably better than even on the initial release, but they have that beautiful vintage look fitting for the era in which the movie was made.