Can a heritage authority exclude an area from the sixty year rule?

Yes. Section 34(3) of the National Heritage Resources Act allows for this:

(3) The provincial heritage resources authority may at its discretion, by notice in the Provincial Gazette, make an exemption from the requirements of subsection (1) within a defined geographical area, or for certain defined categories of site within a defined geographical area, provided that it is satisfied that heritage resources falling into the defined area or category have been identified and are adequately provided for in terms of the provisions of Part 1 of this Chapter.

Subsection 1 is what people commonly refer to as the sixty year rule.

(1) No person may alter or demolish any structure or part of a structure which is older than 60 years without a permit issued by the relevant provincial heritage resources authority.