It sounds very much like that guy is either lying, stupid or a religious nutcase that sees only what he wants to see.
I have lived in Japan for 10 years, was brought up catholic myself & I can tell you there is very little in the way of catholisism in Japan. Christianity is an official religion and there are churches in the cities but it is in no way a national tradition and I still have never met a catholic japanese person. On Christmas eve young couples date and use little rubber things outlawed by the catholic church :P
My ex-girlfriend had a shrine in her house, was registered at the local temple where she went for festivals, special occasions and just to get spiritual advice.
He may be right about the faith thing though, religion and faith are different.
Religion with its written doctrine will inform you what you are to believe. Faith is an actual deep knowing that you trust in your own belief in God. This would mean faith is better
Honestly though, shinto is a recognised religion so he is in fact wrong there.
I am guessing he is catholic and is trying to convert you to/stop you from straying from Catholisism?