Somehow, I doubt any native Muslim community in Japan would face the same kind of persecution as the Christian did. I mean, China has had Muslims for centuries, with a sizeable number of native Hui and other ethnicities, and yet, they were never explicitly targeted by the emperors the same way the Christians, Manicheans or even Buddhists had. And this was with the Chinese Emperor acknowledged as the Son of Heaven, which may seem like a cause for concern for Muslims. The reason for that is because the Muslim communities were borne out of commerce rather than proselytizing, and were never actively seeking to convert the natives or reject the Chinese way of life. They just want to trade and earn money. Contrast that with the Christians, where the temporal authority of the Emperor is actively challenged by some white-faced, pale-haired barbarian priest on the other side of the world, spreading the word of God against the ancient traditions and culture of the Middle Kingdom. You don't get that with the Chinese Muslims, even with their own caliphs.
By that line, any Muslim community in Japan that arises out of merchant trade, which is the most likely, wouldn't be forced underground or exterminated as long as they acknowledged the rule of the Shogun or Emperor (whoever was the dominant power) and more importantly, assimilate as much as possible into the Japanese way of life. Moreover, which Muslim power would bother to actively sponsor conversions in Japan? The Yuan? Maybe, but that Son of Heaven title is a better option. The Malay sultanates? Not strong enough. Mughals, Ottomans and Persia? Can't project naval power that far. So... it really depends what the community does in this situation, but I'd hardly dismiss this as a clear-cut persecution scenario.