I think we can all agree that recording quality, or mastering quality (good mastering generally can't fix a bad recording) is of primary importance over the format. All things being equal, I'm convinced that higher resolution formats sound better. But this is obviously an issue where you have something that was mastered really well off tape at 16/44.1, but then 30 years later they pull out the now worn-out tapes to do a high res remaster, and the mastering engineer hits all the electronics really hot to sound "current", or cranks up the treble because he lost that part of his hearing. You are better off with the original CD quality version in this case.
With the issue of separate masters being on SACDs, I know it has happened, but my sense is that it was not particularly common because it makes zero sense from an economic point of view for a label to pay for two separate masters, when they can just down convert the DSD layer to redbook. All the ones I have owned sounded about the same in character, and with the PCM layer you could tell that it came from DSD.
I've also been doing comparisons in home and studio environments (where I did the recording myself) for almost 20 years, and it's clear there are real differences. It's also clear that higher end DACs in recent times have narrowed the gap somewhat, and a great CD recording always beats a mediocre high res release. I think DSD, if implemented right, is more of a game changer than 24/96, and if I had my way we would have a lot more music at DSD128. But all can be excellent. Of course, I'm just stating the obvious at this point.