They prefer not to but there are some chrons patients on their forum that have the BCIR. Some have been diagnosed after, their UC turned to it after and some had it prior. It is a case by case evaluation is what one general doctor told me when my friend with chrons visited me during my stay. I think it depends on where your issues are. My friend isn't eligible since her problems are all in her small intestines and not the colon.
With that being said most don't do jpouches for chrons either.