My question is about student visa application for non Japanese passport

My son will be studying in Tokyo for one month this year, just at the time he is supposed to apply for his Chinese student X type. Since we are from Europe, my son can enter Japan and stay there 90 days with no visa, but just with a landing permission delivered by the immigration police at the airport. Under these circumstances, will the Chinese consulate in Tokyo accept his application for student X type (non Japanese, and non-resident applicant)?
NB: he will of course be able to present the necessary document including the admission letter from the Chinese school.