Oh sure you can tell if they're from the same master. Why wouldn't you be able to? But that's not the point; comparing SACD layers is invalid … way too many possible variables. As we covered previously.
Oh and Krabapple was being sarcastic in the FLAC vs. WAV thread … obviously. He doesn't claim to hear differences.
We keep tripping over this "same master" issue. It is important, so let me explain.
You make a raw, multitrack music recording in, say, 88k 24 bit resolution. The raw recording is mixed down for stereo and processed - EQ, dynamic compression, added reverb, etc. - into a final stereo master at 88k/24. From that stereo master, a BD-A, say, production master is made at 88k/24 for our example. Also from that same final hi rez stereo master, a CD production master is made via downconversion at 44k 16 bit, possibly using dither of the least significant bits.
I hand those two discs to you and I say compare them with no additional information about the mastering process. There is no way to compare the two digitally to ensure they used the same final master prior to production because of the different sampling rates and bit depths. The bits on the two discs are entirely different, even if it is the same songs from the same recording session. The only way to know that the two used the same final stereo master is to watch the mastering process yourself or take the word of the engineers who mastered the recording and prepared it for final production.
If you listen to both versions and you hear a difference, is that just because one is hi rez and the other one is not? Or, is it possibly because there was not a single final stereo master because the multitrack to stereo mix, the EQ, the dynamic compression, etc. were different between two separate stereo masters - one for the hi rez, another for the CD? If you do not know the provenance of the recording, you have no way of knowing. And, you yourself brought up the possibility that there might be separate stereo masters for the hi rez and the CD some time ago.
In many of the studies of hi rez vs. CD, this problem was avoided by using hi rez music tracks downconverted to RBCD resolution on-the-fly to assure that there was no possibility of multiple stereo masters in the comparison. In other cases, specially prepared versions at different resolutions from the same hi rez master were made prior to the tests by the test administrators to avoid a possible problem.
As I said before, it is unlikely that hi rez and CD mastered and produced at the same time from a hi rez recording session used different stereo masters. Such is also often the case with hybrid SACDs, which contain a CD layer, but it might not always be true, especially with remastered for hi rez re-releases of older CDs. They might have used the original CD master for the CD layer and a remastered version for the hi rez layer. Again, though, trying to hear a difference between hi rez and RBCD is pointless with material originally recorded in analog or RBCD resolution.
Incidentally, Cookie Marenco at Blue Coast normally releases downloads simultaneously at RBCD, FLAC96, WAV96 and DSD formats/resolutions. If you wish to do your own comparisons, this might be a resource, because it is highly likely all came from the same hi rez stereo master. But, if in doubt, just ask hem.