or the operations manual provided by some nitwits
Cheers mate - read my Ops manuals have you? As you can imagine, we write them in an off hand manner with no particular attention paid to RFMs JAR OPS-3 or client requirements.
As has been said, you cannot readily deviate from the Part 1 Section 1 RFM Limitations section, without a statement of 'non objection' or similar from the manufacturer and open discussion with the regulator.
Bear in mind too, that JAR OPS-3 is not law in itself, and it will depend on which national regulator's jurisdiction you are under and what rules they have adopted.
In reality, the RFM content does not tend to figure very highly in the OPS-3 requirements, other than performance, so it may help if you posted some more specific concerns for debate.
What's one of them?