In Orline's Genealogy the surname began the shift from Sension to St. John in the third generation with James.As he called Sention in the town papers but calls himself St. John in his will. It was collusion to say the least as from that generation on the surname appears as St. John. So I can link this to your IDEA of Matthias switching to a phonetic spelling. But this is an assumption.
Has anyone culled the records of Windsor, and obtained an abstract of Mary and Matthias, wedding? Or, Matthias II's baptism?