[JayT]

I don't understand why they would say to lie to customs like that.
You are allowed to study on a tourist visa, but yes you will have to get it renewed before the 3 months are over, it should extend it for another 3 months.

Student visas is for students that study in Japan 6+ Months, since a tourist on a tourist visa can only stay in Japan 6 months out of a calendar year.

Customs in Japan is very fast compared to most places, it shouldn't be a problem at all.

To renew it you must go to an immigration office or leave the country for a few days before the 90 days are over.