Antipsychotics do not treat the flat affect of schizophrenia.
Schizophrenia has symptoms grouped roughly into two clusters--the "positive" symptoms and the "negative" symptoms. The positive symptoms are the obvious, really distressing ones that you probably associate with schizophrenia, things like hallucinations, delusions, paranoia, disordered thinking. The negative symptoms are things like flat affect, as well as poor motivation, poor concentration, executive dysfunction.
The antipsychotics are useful for the positive symptoms of schizophrenia. If you have schizophrenia and you take an antipsychotic, and it works, you start to be able to reality-test better; your delusions fade, your hallucinations become less severe and easy to ignore, or even vanish altogether. You find it easier to think logically.
However, the negative symptoms are only affected slightly, or not at all. You may still have problems with motivation, with emotions, with self-regulation. You might have trouble starting and stopping activities. You might not express the emotion you feel, or might not feel emotion strongly. The longer your schizophrenia went untreated, the worse those problems tend to be; quick treatment can sometimes prevent them altogether. But you'll probably need counseling to help you deal with those things, to learn coping skills and get back to your life as you recover from a psychotic episode.
For autistic people with flat affect, I wouldn't think that antipsychotics would be particularly useful. The only thing I've seen them used for with any success among autistic people is essentially as a tranquilizer for people who are so anxious, or so prone to meltdowns, that they are severely impaired. But even then, sometimes the antipsychotic is more of a cover-up than a solution. Both anxiety and meltdowns respond best to therapy that involves figuring out why they happen and how they can be prevented; and anxiety is often better addressed via an antidepressant rather than an antipsychotic. If it really comes down to a choice, the question is: Are the symptoms you're trying to treat worse than the effects of the antipsychotic plus whatever of the symptoms are left over once you start treatment? For autistics, often times the answer is that antipsychotics make life better for your caretakers, but not for you, because they keep you from learning or paying attention nearly as well as without them. And there are other options that don't have such problematic side effects. Those should be tried first, as they're preferable in just about every way to simply sedating yourself with an antipsychotic.
Flat affect, by the way, is probably best treated through therapy--specifically, social skills lessons and lessons in using facial expressions, plus a lot of practice. Facial expressions are just another form of communication, and that's something you can learn, just like you learned to write or speak. It may not come naturally to some of us, but it can be learned explicitly. If you have a tendency to have little or no emotional expression, and you want people to be able to see what you are feeling, you can study facial expressions and learn how to use them.