Next time you apply for a certificate, you should insist that CASA apply and comply with the provisions of 67.150(6). If you pass any one of the 3 tests listed in 67.150(6) you have demonstrated compliance with the colour perception standard. Provided you meet the other aspects of the medical standard, you are entitled to a ‘clean’ certificate.
Any note on your certificate in those circumstances is as relevant and valid as a note that says “The holder is left handed”.