It is highly unlikely that he ignored the very relevant words of the chok yaakov which are on the spot here. He is most likely referencing the second teretz that only if it falls in by itself is it batel.
Furthermore, in the שער הציון he refersus to ש"א. it is ידוע that this usually means the Gra"z, and the Gra"z clearly is choshesh for the second teretz of the חק יעקב.
This is pure conjecture and projection. And ש״א does not mean Graz.
He is מעתיק the מג״א and מחצית השקל. They seem to be learning that there is no rov against the חרדל so the question literally doesn’t start.
The חק יעקב is going on the case of the מהרי״ל, the MB doesn’t elaborate on that at all.