I think the only proper test would be to run both movies through two identical players using a switcher.
Godfather 1/2 are the only BR's that I have two copies of, so there's never been cause for me to question whether this could be an issue or not.
The only other film I've had multiple copies of was Star Wars on DVD. I had to return my first boxset because the opening crawl on ep. 4 had noticeable artifacting. The second copy was perfect.
I bought the SE SW with the unaltered movies as a bonus and the colors had been changed noticeably, esp. skin tones.
It's likely that the sapphire releases and the boxset BR discs are identical, but I clearly prefer the sapphire "versions."
I switched out the discs (Pt. 1) and compared scene 5 on both. The posters here are probably right, but I def. prefer the standalone sapphire version. Odd, isn't it?