Autos generally don't do that well outdoors, they really need 18/6 to perform reliably/decently.
Also, by not filling your pots right up and having the seedlings sitting so low and deep down has restricted the amount of (reflected) side light they received when young, leading to (possible) diminished growth.
The full pots of soil also provides vastly more room for root growth. More roots = more plant.
Autos are probably the biggest disappointment for the outdoor cultivator, they just don't get enough light to grow to a decent size before flowering starts. This is the reason I stopped growing autos, poor yields and with no real advantages over photoperiod plants.
On the other hand, you can plant seeds every 2-4 weeks, right up to the end of July, and have an ocean of one foot plants if you are happy with that.
Hope this hel[s, Organoman.