I would say that under this, people who are applying for refugee status from outside Canada are specifically excluded from this. And it appears, because this legislation keeps referring to applying for a visa, that refugees inside Canada who are accepted are not applying for visas. So it appears that it does not affect refugees.
Evidence of meeting #41 for Citizenship and Immigration in the 39th Parliament, 2nd Session. (The original version is on Parliament’s site, as are the minutes.) The winning word was c-50.
A recording is available from Parliament.