I find this to be a bit silly to post about, but it is a decent question. Many people are confused about the culture of the Pokemon world. I don't think Satoshi Tajiri was trying to be confusing when he made the games. This is what I think about the Pokemon world;
I think that the "Pokemon World" is the real world, only with the Unnamed Pokemon nation in Japan's place. I've posted this theory many times, but it is understandable. The architecture, customs, and personalities, are very reflective off of Japan. However the culture is strongly based with Pokemon and this is reflected in the training, battling, and raising.
I believe that Christianity and Buddhism still exist, as do other countries. Now I agree that perhaps "The Nation" does worship Pokemon, but perhaps a demographic believes in other theological ideas. If I were to lived in the fictional regions, I would probably worship Mew.
Anyways, I think that your question is interesting, and as for the "Church", It is called the Foriegn Building, but if you look at their glass art, you can see what appears to be the "1 and 3" symbol.
That's all for now-
Sinerely
-ChrisTom