Most of the members of my Tuesday group belong to a guild that supports a preemie project and I have seen their projects and contributed a couple of tops. They have guidelines to follow, like they don't want just solid pieces of fabric so there should be some seams but not too many or too bulky. It is always flannel on the back, most tops are cotton but can be flannel. And they use batting, a specific cotton batting if I recall but I'm not sure on the content.
Here in the Northwest, I think most quilters would use batting between flannel. I don't use flannel for myself because I have too many pet hairs floating about and there are few things worse than pulling a cat hair covered piece of flannel across your mouth while you are trying to sleep!
The guild I used to belong to supported Ronald McDonald House as well and we had many different variations on fabrics and battings, at that time the key was washability and durability. Personally, I mostly like fairly high loft poly batts, but I think for an all flannel quilt I'd be looking at a low loft, basically something to hold the stitches in (like I recommend putting in a piece of flannel between fleece backs and tops). I have a hard time imagining an all flannel quilt on warm and natural, but I think I'd be looking at fairly simple 30s style blocks for inspiration in that way.
Some of my donation projects may not look all that impressive completed, but often they are amazing when how it started as raw ingredients.