I think you misunderstand some of the relationships between laws, decisions, and justifications, and you're conflating two separate areas of jurisprudence. The linked real-world example you provide is happening in the employment context, but also in a government context (since it is a public school). But all the examples in your list have nothing to do with employment law and would be purely statutory/regulatory prohibitions. I will attempt to answer broadly enough to cover both domains.
Laws and regulations can be challenged as discriminatory
The things you have listed under "decency law" would be criminal or regulatory matters. A preliminary question would be whether the laws as written even capture the behaviours you've described. To the extent that they result in discrimination, the laws could be challenged as breaches of s. 15 (right to the equal protection and equal benefit of the law without discrimination) of the Canadian Charter of Rights and Freedoms. There may be other Charter arguments too, if the laws affect expression or life, liberty, or the security of the person. (Public decency / nudity laws are more frequently challenged on grounds of free expression.)
Decisions of school boards are subject to the Charter
The Charter almost certainly applies to decisions of public school boards and schools. See Elementary Teachers Federation of Ontario v. York Region District School Board, 2022 ONCA 476, paras. 39-41. These decisions could be challenged by judicial review (i.e. court review of an administrative decision-maker's decisions) and would be analyzed for reasonableness, including whether the decision strikes a proportionate balance between the Charter right and the statutory objectives (Doré v. Barreau du Québec, 2012 SCC 12).
Even if there is an infringement, the government gets a chance to justify it
If you're looking for some sort of a "line" it is found in the justification or reasonableness analysis.
Where a law or regulation is challenged, and if a breach of s. 15 is established, then the onus is on the government to justify the breach as a reasonable limit as allowed by s. 1 of the Charter. This will depend on the importance of the government objective, whether there is a rational connection between the objective and the law, whether the law is minimally impairing, and whether the impact on the claimant is proportional to the salutary effects of the law.
When a court reviews an administrative decision for reasonableness, it is "engaged in balancing somewhat different but related considerations, namely, has the decision-maker disproportionately, and therefore unreasonably, limited a Charter right. In both cases, we are looking for whether there is an appropriate balance between rights and objectives, and the purpose of both exercises is to ensure that the rights at issue are not unreasonably limited" (Doré, para. 6).
In each of your examples, the judgments would be highly fact-based and it is fruitless to speculate about what the evidence might show.
Relevance of association with minors
You ask whether it would matter "if the person in question was primarily associating with minors." This likely would not matter if a law was challenged, because such challenges are about the validity of the law, not the factors that might render its applicability to a particular person to be more or less justified. But if the law itself had the purpose of protecting children, or if the law itself was targetted solely at those associating with minors or those in positions of authority over minors, this would be a factor weighing in favour of justification of the infringing law (Irwin Toy, R. v. Sharpe). Whether the person in question was primarily associating with minors would matter in the context of an administrative decision, because these decisions are case-specific.
Some anti-discrimination statutes provide more protections
Ontario's Human Rights Code potentially contains even further protections. Section 5 says that every person has a right to equal treatment with respect to employment without discrimination because of sex, gender identity, gender expression, and other enumerated factors. Section 24 provides for exceptions to that right in educational settings (and some others) where what would otherwise be discrimination is actually a bona fide qualification of the employment and if it cannot be accommodated without undue hardship on the employer. These judgments are also highly fact-based and it would be fruitless to speculate about what the evidence might show.
