When Francis Xavier arrived in Satsuma he began to explain the tenets of his faith to the local Dayamo through an interpreter. The lord, upon understanding the outline of the Christian doctrine presented, nodded and stated that he was familiar with the faith; as his brother had taken vows at a local monastery and when he came to visit he spoke at length on his religion.
(something about the tone made it clear how great the length was)
The Lord of Satsuma then instructed Francis to speak to the local bishop if he wished to preach or establish any religious houses.
PoD: In the late 8th century, Nestorian clerics arrived from China and established a small number of monastaries in Heian Japan. Through a combination of luck and clever political maneuvers neither the native Shinto nor better established Buddhist clergies suppressed them as the Tang authorities did in China, although they grew increasingly heterodox and isolated from the rest of Christiandom. By the 1500s it was no more out of the question to light candles at a shrine to the Nazarene than it was to do so for the Gods of Fortune, but those who politely refused to acknowledge the divine decent of the Emperor (merely praying for his wisdom) was somewhere below 10% even in the strongholds on the western coasts.
In short, a heterodox branch of Christianity is a long established part of the Japanese Religious Melange before the Catholic missions even arrive. Ramifications?