CRA seems to acknowledge that it lacks discretion to not apply the provisions of the ITA as judicially interpreted
Regarding whether, following Collins, CRA considers, with the exception of provisions explicitly conferring discretion, that it has no discretion regarding the application of the Act, it stated:
In Collins, the Supreme Court of Canada recognized that the Minister and the Minister’s agents "are required to follow [the Act] absolutely, just as taxpayers are also required to obey it as it stands". It follows that where the CRA assesses a taxpayer, it is required to do so in accordance with the facts and the law. In this context, we agree with the conclusions of the Supreme Court of Canada that, when it makes an assessment, the CRA is bound to apply the directive set out by Parliament in the Income Tax Act, as interpreted by a court of law, provided that interpretation has not been found to be incorrect by a higher court.