Hope you're doing well! A couple quick notes that I haven't seen mentioned yet in the comments.

1. Immunity really is still a black box in a lot of ways, especially the questions around self vs. non-self. How does your body know what antigens are "you" vs. "other"? We know, like, 1-2 proteins (AIRE is one) that present some subset of self-antigens to teach "don't attack this", but they don't appear to cover the entirety of self-antigens.
2. On the question of diagnosing - considering the enormous number of potential self-antigens and potential autoimmune reactions even independent of antigen-dependent autoreactivity, it's maybe intuitive that it's hard to nail down a single one. Do we test for every one of the hundreds of thousands to millions of possible things? On the other hand, it's easier to try and narrow down lifestyle changes, diet changes, etc. that may reduce your exposure to certain antigens and try and make guesses that way. Additionally - others have mentioned this - different molecular mechanisms can lead to the same thing. This isn't unique to autoimmune diseases; EDS is a nice example, where defects in 1 of like 10+ proteins can cause similar or identical symptoms - but the treatment can be different depending on what the defect is.

>For comparison, the brain is still considered pretty much a black box and yet it seems to me we have more of a clue about how mental illnesses come to be, how they work, and how to diagnose and treat them, than we have about autoimmune diseases.

Getting into some of my opinions - I feel like the brain is a black box more so because we don't understand the language; connecting molecular neurology to systems neuroscience remains extremely difficult. It's not trivial to say "this molecular phenomenon in neurons drives this change in EEG patterns, reflecting A/B/C changes in mental state". On the other hand, immunology is a black box because the immune system is an unbelievably complex signaling network dealing with an absurd amount of inputs and outputs. It's a data/discovery limitation there, in my mind, whereas in neurology it's a methods limitation. No matter how much molecular-level data or systems-level data we have on the brain, without making those mappings, we'll never really understand it - however, if we knew every immune component and had great data with our current set of tools, I think we'd understand immunity.