The clue is in the old catch all....
Notwithstanding anything contained in any of the company manuals, the Commander may deviate from these procedures when he believes it is necessary for the safety of the flight etc
If you have a problem which restricts your MTOW it would be prudent to ignore the MEL and taxi back in.
If the aircraft will be AOG at Much Snoring in the Middle of Nowhere when it lands with a fault, and there is no tech support available, it be may preferable - commercially - to RTB.
And so on......that is why the Commander gets paid so little
