Hi Mark,
I am NOT very knowledgeable on this area at all, but my instincts would be to agree with you - why should the B2 software decode the output of an attached USB CD reader in a different manner than an internal (essentially USB) CD reader. The data flow coming into the Pi inside the B2 should be the same for the same disk.
Much more likely is that the recent quality degradation experienced with the current batch of B2 CD Readers is the problem.
Looking at the data I have from the problem albums AND RIPPED ON MY 2016 B" with the latest (non test) B2B software,
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and or
Do not have any distortion and play fine.
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Thus the empirical data backed evidence would seem to support my contention that "CDs, in particular, have some sort of copy protection built-in and this appears to cause the distortion problem." is, with all du respects to Martin Brennan
a red herring.
Fred