There's apparently a fair bit of evidence to suggest that IBD is indeed autoimmune, ie where the immune system reacts to your body tissues rather than just the foreign bodies. There's still debate on this front since modern medicine still can't explain a great deal about how it all works, but looking my own case, I think I agree with this hypothesis.
My immune system has always been overactive, but until the chronic illness came along, this was just an advantage as I was never sick for long. That said, I know many others that have the opposite response to me, ie they've always had an under active immune system, as people have already posted here.
As for the extent of the autoimmunity, the frequency of the linkage of IBD with autoimmune/autoinflammatory skin conditions such as pyoderma gangrenosum, erythema nodosum & psoriasis and others such as rheumatoid arthritis & psoriatic arthritis would probably suggest that it's not always quite as localised as many of us may like to think.
It's probably a pretty good assumption that the immune system is involved somehow, and IBD probably meets the definition of autoimmune, as the successful use of immunosuppressants would suggest. However, as for what that actually means for individual people, everyone is different, and will often be contradictory, as is usually the case with discussions about IBD etiology.
There is still a lot of work to be done in regards to IBD etiology, but the same can be said for a lot of the current autoimmune or autoinflammatory conditions. It seems modern medicine can't yet explain the mechanisms behind these conditions as much as we'd like it to.