Why would we universally acknowledge something that is factually and legally incorrect?

I am an atheist but Canada unlike the US has not constitutionally entrenched the separation of church and state.  There are no clauses in our Constitution Act of 1867 and we have no counterpart of the First Amendment of the American constitution. 

Our constitution actually mandates state funding of "separate schools" (Catholic or Protestant minorities only not other religions) in several provinces and that is constitutionally valid.  That would be anathema in the USA.  See  Adler v Ontario (AG), [1996] 3 S.C.R. 609

In fact as PM Harper correctly noted in an interview several years ago the separation of church and state is an American constitutional concept and does not apply to the Canadian constitution. He went on to say that separation of church and state in Canada has meant, traditionally, that the government will not interfere with religion.