The Sakoku policy was pretty much Universal, the Japanese traded with the Ainu and Ryukyu's on account of both being partially Japanese (and thus indirectly traded with some other using them as mediaries) and had highly regulated trade with the Dutch, Chinese and Koreans through a few specific places.
Foreigners, regardless of religion or place of origin were not allowed to enter the country (save for the aforementioned designated trading places), nor were the Japanese people allowed to leave Japan, so you could'nt have transmission via converted natives either.