I'll answer from my own viewpoint of having Hashimoto's thyroiditis, an autoimmune disease targeting the thyroid, which is destroyed over time by antibodies. I also have histamine intolerance and allergies, my immune system is very reactive, too reactive!
We don't fully know why autoimmunity develops. It could be a combination of triggers, including genetics, diet, viruses, exposure to chemicals/heavy metals, injuries, disturbance to the gut microbiome, etc. Each one of us is different with respect to the cause(s) of our disease and its progress. Autoimmune conditions often 'hunt together' and if you have one you are far more likely to get more. Also just being female makes one far more susceptible for reasons not fully understood. Autoimmunity often runs in families, too. My mother had thyroid disease, so do I. Her mother had RA. My mother had RA. I am praying I don't get it too.
Even though I should be able to sort out my hypo symptoms by taking thyroid hormone, that won't sort out my autoimmunity. Doesn't help that I haven't been able to get my hypo under control, but that's another story.
I believe this is why we have to be very cautious when putting anything into our bodies, from the foods we eat, any medications we take, and of course, having vaccines, because any of these things can be triggers. Of course some folk with autoimmunity (such as lupus) must take drugs that end up suppressing their immune systems, so that is yet another risk factor that may tip the balance between not having a vaccine and having it.
We need more data!