It's his decision. Autism or no, it's Junior who has to decide to comply. All teens seem to willfully ignore their parents' good advice. Severe acne calls for isoretinoin, which he may well accept even if he won't use a topical agent; oral antibiotics must be used with a topical. Junior needs to spend time alone with his personal physician, during which time they can talk about acne or whatever. You must let go.
Ask your derm MD. Acne has different modes of treatment, ranging from topical (applied to skin directly), medical (oral drugs), and nutritional (foods to avoid or to encourage). Discuss with the dermatologist the different options for each mode of therapy, then make your decision based on your child's known likes and dislikes.