As I understand it.

It goes by your craftsmanship, as hq chances go by your control. The higher your craftsmanship the less likely you are to botch. But CS is a weaver skill you learn that gives auto 100% success. Autocraft goes by the standard synthesis moves, which have a chance to fail even if they are 1 and done. You can get that craftsmanship high enough to basically make it 100% but unless they changed it, it will cap somewhere around 99% success. It's the chance you take in mass production. Still saves you an immense amount of time when hq isn't a concern.