I would recommend that he fill these fields to the best of his ability, following rather the spirit of the question than the literal letter. The first question he would need to leave blank. For the second question, he might be able to compare you to actual students he did have - if this is not meaningfully possible (e.g., if he is an industrial researcher, who never had any students), then he should leave that one blank, too.
He should then point these questions out in his recommendation letter and explain why he could not enter anything there.
The problem of course is that you don't know whether these online forms are first processed automatically, and whether blank fields could count against you without a human even parsing the explanations in the recommendation letter. I would assume that such issues arise frequently and that the people who create such forms are smart enough to understand this. In which case I would assume that blank fields are treated separately and do not lead to an automatic exclusion of your application.
(Of course, it could be that if a "large" percentage of blank fields could indeed be an automatic rejection, since one could argue that the recommender might not even know you well enough in an academic context.)
EDIT, in the light of xLeitix' answer: I realize that I answered based on the assumption that these questions are multiple choice questions, not free text questions. If these are free text questions, then yes, he should answer truthfully that you never were a student of his (and still go into details in his recommendation letter).