I mean, the point of rights is that they are inalienable, not that they are subject to the whims of the government of the day.
I would suggest requiring Canadian citizens to provide personal health information via an app and submit to testing to avoid confinement when entering the country are an abrogration of that right.
All Charter rights are subject to reasonable restrictions, which can be arbitrated through the courts. References to "inalienable" rights is a term used in the US Constitution, not the Canadian Charter of Rights and Freedoms. The concept that the federal government cannot ask health questions of those travelling internationally in the middle of a worldwide pandemic, because the administration of healthcare is primarily a provincial responsibility, is IMO just a "talking point" by those opposed to it.
If it is solely a provincial jurisdiction, why do we have the Canada Health Act and why did the recent meeting of provincial premiers complain that they need more money from the federal government to fund it, which I happen to agree with? Very little is cut and dried in terms of jurisdictional responsibilities between the federal and provincial governments, since we mostly have an integrated tax system and a national criminal code, as well as a national health act. Until it is challenged in the courts and a ruling is made by the Supreme Court of Canada, it is still a legitimate regulation we all must follow, whether you agree with it or not.
We did not have an integrated, national, public healthcare system until 1966, when the Canada Health Act came into being. Prior to that, under the original articles of confederation, originally known as the British North America Act, 1867, now referred to as the Constitution Act, 1867, the provinces were responsible for the administration of most hospitals, sanatoriums charitable institutions, and the like. The federal government was responsible for "quarantine and the establishment and maintenance of marine hospitals", so your argument is very muddy.
In the meantime, if everyone did their homework and followed the rules, it might help all of us when travelling internationally. If you don't think it's right or fair, then complaining to your MP and MPP/MLA/MNA is probably a more productive route, IMO.