Your experience is not uncommon for individuals with spasmodic dysphonia. While Botox can be a very effective treatment there is also a lot of room for error because the area around our vocal folds is also responsible for keeping things out of our airway. That must have been a scary experience to go through choking on your saliva. Spasmodic dysphonia is a dysfunction of the vocal folds so they don't close together while speaking causing too much air to escape through the vocal folds when phonating. There certainly are autoimmune disorders that can cause voice disorders and other speech and language impairments. There are a few things that can lead to SD to the nervous system causing tremors in the body, dystonia a brain disorder that causes muscles to be very tight and in more rare cases prolonged severely prolonged exposure to stress. SD can certainly be connected to autoimmune disorders depending on the symptoms.
It's unfortunate that people equate speech ability with cognitive function. This is very common for individuals with variety of speech and language impairments. I highly recommend seeing a speech language pathologist if you haven't already done so recently. You can get a referral from you ENT. There are some fabulous clinics around the US that specialize in voice disorders which I highly recommend. While SD is not curable it is possible to learn techniques and strategies that can improve communication.