Actually, if you look at transitional provision clause 127, it's written:
Despite section 13 of the Canada Elections Act, as enacted by section 3, the person who occupies the position of Chief Electoral Officer immediately before the day on which that section 3 comes into force may continue to hold office until he or she reaches the age of 65 years.
So there would be no transitional provision to remove the non-renewability of the CEO's term.