But, surely if Chris was Clark's son, they would have noticed something unusual about Chris' biology after nearly a year and a half worth of doctor baby check-ups? In the absence of anything peculiar, Clark should be able to rule out Chris being biologically his. I can't imagine Kryptonian genes being slow active enough so that all doctor exams up to this point would be have ruled out anything unusual.
I agree that for this Clark it shouldn't matter, but I think Clark is working on a pretty safe assumption that Chris is not biologically his.