Great pic, PSparkle!
Don't worry, we have all freaked out on this wretched voyage of the Anal Fissure (had this for over two years now).
I would not worry about an autoimmune disease unless you have been diagnosed with one, or you have something else going on that you think is more than the fissures. I have Behcet's Disease, but it has nothing to do with the fissures. A bit difficult for me to go into the inns and outs of it, but you can have a look on the web. I don't have the most serious variety, and don't take strong drugs for it. It did not scream out - had a few symptoms for years and years and did nothing until I got quite ill with mouth ulcers.
I have not had a colonoscopy (don't want to), and CRS are pretty loathe to give younger people like yourself these unless they think cannot find an answer, hence why your doctor possibly wants to do that. (Is this a colon and rectal surgeon, by the way.) I have, however, had a sigmoidoscopy and an anoscopy. Anoscopy hurt like hell, but for the sigmoidoscopy I had a sedative and it was done in hospital. All they came back with was diverticulosis, hemorrhoids and healing fissure. Have also had an MRI and a CT scan.
Abdominal pain is not a common feature of fissures, but could be diverticulosis, as I get this if there is a flare-up from me eating something that irritates. I watch my diet carefully...very boring, but necessary.
Hope this helps a bit. Sorry you are going through all this