Now I am in no way an expert. I don't represent "real" Christian books, and not just because I am a heathen, but also because I wouldn't know where to begin selling them. There is an entirely separate group of publishers and editors and bookstores and writers (and agents!) who are "CBA", and these books are often not even found in regular trade bookstores... well, at least, not much in San Francisco. ;-)
I do see lots of trade YA submissions about teens struggling with matters of faith, and I find those very relevant and interesting. I'd be happy to see more of this kind of book. However a word of caution: it is very easy to cheat and start stereotyping people for comic or dramatic effect. After all, it's easy to hate two-dimensional cardboard zealots.
Most submissions with religious themes that I see show super-religious folks as misguided cuckoo-birds or worse, straight-up Evil. (Sometimes, to mix it up, they'll be Perfectly Good with no shades of gray.)
But that is not my experience of the real world, and it probably isn't yours either. Think about people who are hardcore about their religious beliefs, including most Catholic priests & nuns, Buddhist monks, Christian Fundamentalists, Mormons, Quakers, Orthodox Jews, or whatever... the vast majority are pretty cool and nice. Or, if they are jerks, their religion doesn't make them so; they would be jerks even if they were Atheists. They also generally think about lots of things besides religion, and have other dimensions to their personality, sometimes even conflicting ones. And that is actually where the drama and interest is, to me.*
(A really excellent YA about matters of faith: EVOLUTION, ME & OTHER FREAKS OF NATURE by Robin Brande)
As for the difference in picture books between the two markets, my old pal Editorial Anonymous said it best:
Christian for trade:
Santa being jolly
Jesus being born
The spirit of giving and how you want it in you
Christian for Christians:
Santa being too commercial
Jesus doing anything else
The spirit of God and how you want it in you
* ETA: Also, despite popular opinion, most priests are NOT child molesters. Seriously, you think we could give that trope a rest?