I would state that you should explain the issue. Also give them the email and telephone number to reach them. I think a lot of folks forget that visa officers review on a case by case basis. You could have the correct format of reference letters AND STILL get rejected. Inversely, you may have digressed from the original format but with an appropriate explanation and supportive documents for evidence you can STILL be approved. Nothing is written in black and white especially if you don't have a representative. Actually, you have more flexibility if you don't even have one. The VOs understand that challenges may arise. Your duty is to convince them in the veracity of your claim.
Most employers are unwilling to follow that format provided by CIC. Why? Because the employer has their own guidelines, take it or leave it. So you as the principal applicant has to fill in that gap through explanation and providing further evidence.
