212man is spot on (he usually is
)
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.
As a pilot you should follow your Ops Manual, published checklists, etc but you always have to follow what is printed in the Limitations section of the RFM.
The Company you work for has the option to deviate from the rest of the RFM if it chooses to do so, but unless any deviance is agreed by the manufacturer then there is always the risk that it can be challenged by the lawyers should something go wrong!
A pilot will expose himself to challenge by the lawyers if he doesn't follow Part 1 Section 1 of the RFM or your Company published procedures.
Simple really
It has to be otherwise line pilots wouldn't know what to do
(just redressing the usual management/FOI bashing that goes on!!)