How do you access the modded religions. They never seem to appear in-game.
There is a bug when you are playing one of the included maps that prevents access to the new religions. I've fixed this for 0.6. The new religions work fine on generated maps.
Also, why for the scenerios are you alowed to choose non-scenerio civs?
The scenarios aren't actually scenarios. They're maps with a python script to assign the starting locations and allow free choice of leader. A side effect of this is that you appear to get free choice of civilization as well, though if you try to play as an unsupported civ that map will give you an error and revert to randomized civ selection. There's no other way no way around this sorry.