Well, depends. It certainly can be used in a variety of situations. The basis of the notwithstanding clause doesn't require that rights be set aside, it can be used to identify that an interpretation of rights is incorrect. For instance, where rights have been determined in the outcome of a case that isn't deliberately mentioned in the relevant act, it would be perfectly acceptable for parliament to use the notwithstanding clause to say "no, that's not what is written in the law we wrote." The 'threat' of using the notwithstanding cause in Ontario recently in the Ford government is a good example of that. They ended up not needing it because the courts determined that the original ruling was probably 'wrong' before it was needed...

In this case, gender expression is a right that has been established repeatedly despite it not being explicitly mentioned in Section 15. (1) of the Canadian Charter of Rights and Freedom (the basis is that gender expression is related to the sex of the individual). So, it 'technically' could be used correctly in this situation, but they are certainly assholes for fighting people for expressing their gender when it has been firmly set outside of the language.