I think this is a fantastic idea; and something Unity sorely needs. I found modeling simple rooms and shapes in Blender a chore, especially when it comes to texturing. Sometimes I don't want to unwrap, and it'd be nice if I could just apply textures to a face like in Hammer, and be able to stretch geometry without the texture stretching with it.
Rather than having a custom level file format, wouldn't it be better for the program to output a model in a few common formats? That way, you've got a truely generic and cross-engine level editor basically from the get-go with no implementation necessary.
Either that, or you keep the custom level file format, and have an export function that can save the level in one of a handful common model formats.