A duplicate submission merged with an existing Pokéstop?

Yes, if they are interesting in their own right.

It is hard to draw the line as to where a stained glass work starts becoming a work of art and stops being just a window, which would be infrastructure for the church, and would not be eligible separately. The more you can find out about each piece, the more likely it is to be accepted.

Here is a general clarification on unique art: