I think both Crohns and MS are autoimmune diseases, but other than that, I don't know that there is a directly link. Not all of us with MS also have Crohns, or another autoimmune disease.
There ARE bowel problems associated with MS, though. Not everyone with MS experiences bowel problems, but for those of us who do, there is some consistency: it's a matter of bowel sluggishness. The bowel is a muscle. It contracts in a rhythmic pattern, expelling waste. If the nerve signals don't get through to the bowel from the brain (because of a lesion(s) in the wrong place), then the bowel doesn't work properly. Bloating, constipation, bowel incontinence, cramping -- all those kinds of things -- can result. But these are different than the issues with Crohns disease, although they may look similar from the outside.
I can't help with your question about brain atrophy. The pictures that I've seen seem to indicate that it is not just a particular part of the brain that shrinks, but an over-all shrinkage. But I really don't know.
...I am not a doctor, nor health professional, and don't pretend to be one, here.....