I'm not sure how the common law spouse thing works, whether you had to disclose him because you lived with him over a year or not. I leave that to someone who is in the know.
However, as i see it, you could have just left him off your application, you're not married and he has his own pathway to PR through his study permit and PGWP. So his legal status in Canada is not tied to yours.
Now that you've declared him, it's very difficult for you to justify that he's not accompanying you when he most likely will want to stay, and the immigration officer knows this. The only thing i'd say is emphasize that he has his own legal status in Canada, and because you're not married, he intends to either make his own application for permanent residence at a later date or return to his country of origin after his studies are completed.
I think at this point, it's better to emphasize that he wishes to have his own, separate application based on his decisions on whether he wants to remain in Canada or return to his home country, and this is not a decision which he has made yet. Emphasize you disclosed your relationship for the sake of completeness, but that you are determining your respective immigration statuses separately.