As far as I recall--correct me on this, Mark--in the Canada Health Act there's no exemption for Quebec. Also, the Canada Health Act does not provide for funding directly; it actually adds to conditions that might exist in other legislation that does provide funding. So it simply adds conditions to existing payments.
Bill C-303 might be the same purpose, which is to attach conditions on transfers otherwise appropriated by Parliament. The difference with the Canada Health Act is that Quebec would be exempted, meaning that any funding Quebec might receive under acts of Parliament could go on, even though Quebec does not meet these additional criteria conditions. That's one way of reading the legislation.