Well, the only exception that is mentioned, is contained in "2.3.1", and has to do with airline staff/ID travel.

As for "incompatible procedures", I believe that it is only "incompatible" in practice, because the airlines do not want to incur extra costs. When it comes to non-endorsable/IT/award and similar tickets, here's my understanding of how it works:

Airline X (the original carrier) calculates a cash value (say $100) on the ticket coupon for the segment, which, for such tickets is typically quite low, compared to the published fares (say the full Y fare is $500).

If airline Y (new carrier) is a part of the same alliance, they have no choice, but to accept the $100 and fly that PAX (at least that's how *A works).

The fun starts when airline Y is not a part of the same alliance. They may look at $100, and say "no way, we want more!". Airline X, then has to increase their offer, up to the point when airline Y agrees to accept it.