Do you know how much Endorphin costs? I should think it's quite expensive so if you're spending that much you might want to shell out on something extra for the graphics engine maybe?
Actually I don't think Endorphin is even licensable these days? According to their site, they send off employees to work in-house with the development team. So I highly doubt they will work with a small indie development team.
Ok, so your answer is yes it will work with irrlicht, it's completely seperate to irrlicht, irrlicht just renders, naturalmotion does other stuff (physics and/or animation right?) which can compliment it.
So it's just a case of figuring out how to integrate the two, feel free to take the first steps and share your findings with the community