If the Ops Manual contains any matter which is contrary to provisions of the Act, Regulations or Orders, then the Act, Regulations or Oders shall prevail - not the Ops Manual. CAAPs are advisory documents, not legislation.
I am not sure that is the correct interpretation here are a few examples
You company ops manual says the company TO minima is 200m yet this is way below the minima published in the regs which takes precedence?
Your company has an approval in the ops manual to fly 12 hour duty day which is beyond the regs which one is right?
If ops manual says to add .1 per landing yet the regs say start to shut down on a ramp check what is the FOI going to say?? And the answer is follow the ops manual because I have had this very thing happen!!!