I never owned the Sony DVD, so I wasn't aware that it included the extended cut. Anyway, I'm happy that those who prefer the Amfitheatrof score now have the opportunity to have available on the Arrow Blu-ray of the extended cut.
Back in 2013 Nick Redman explained that the Blu-ray master of the extended cut that they received from Sony contained only the Caliendo score. It's possible that in 2013 Sony had not yet re-worked the Amfitheatrof score to fit the extended running time.