Same time it's best to top any plant... and that depends entirely on your goal for the canopy. With autos, you have to guess as to how much remaining vege growth you'll get. That's the only difference.
Probably better not to top autoflowers, as they tend to be small plants and you don't control vege time, so anything you cut off is lost yield. Cuttingn off a node or two when topping is not a significant loss, of course, but still loss relative to not having any control over vegetative phase length. Better to just spread it out with training. The yield is primarly dictated by the amount of light and atmopsheric co2... what we control is merely reaching that potential. i.e. don't step on your own dick/flaps and it'll turn out fine.