The proto discovery probably gave them a little bit of leeway to be like "aha, you see! The replacement tracks were the intended tracks all along!" which gives the whole "they replaced the music, those bastards!" scandal a little more positive spin. Of course, you'd think someone at Sega internally would have known that already, but given their track record of documenting/preserving historical stuff, I'm highly doubtful. The line always seems to have been that the PC release changed the music.