Yes, you can buy a single family house and convert it to multi-family using
renovation funds through a NACA mortgage. However, your are legally still buying a single family home, and it will be considered such until the renovation is done and the legal status of the property is changed to a multi-family. Therefore you will be limited to the single family purchase limit.
Since HAND Department rules say you may borrow up to 110% of the post renovation value, you may find more renovation funds available than normal. Please contact the HAND Department directly at 210-319-2978 with specific questions.