Maybe I"m wrong here, but well his scratching himself like that... it is OFTEN or can be a sign of stress or frustration.... or a way for the child to "cope" with something they are not happy about or cannot handle. This is how kids express stress or frustration, or being irked.
So go by this cue he is giving you... and give him space.
No, AP parenting does not lead to dependency. But the child also needs to have their own space and allowed to do things on their own too...
I am AP... but I also greatly nurture my kids own personalities, versus mine and I teach them to know themselves. They are really great self-reliant kids and can communicate feelings well, for their ages.
My son, who is 3.5... will even tell me "I'm grumpy... I want to be alone..." then I respect that. That is how HE is. Then after he is fine, he comes to me and gives me a hug. He knows himself. He simply needs space... when he is grumpy... instead of me interfering in "his" own way to unwind. Many adults are like that too. I go by my kids cues and personalities. While still being very AP with them and loving that way. I am not A. AP purist.
Maybe, instead of anticipating your child's every need... just let him be.. give him space... let him know verbally you are there for him... but just try let him hang out and "be." I am not saying you are wrong or your AP parenting is wrong, because I do that too... but, you said you "anticipate his wants & needs...." but that also hinders a child's development as well. Because... THEY need to experience themselves and learn how to feel and communicate. But NO, it does not create dependent kids. Again, I do not agree with your Ped's statement of that. It is NOT about making the kid "in control". Your Ped does not understand.
I think.. your son has full capacity for affection etc., but maybe he gets so much of it that he may feel overwhelmed. Kids/babies get "irked" too... ya know.
But, his aggressiveness with is teddies etc. may be just boy stuff and or not. Or just frustration...
And at this age, a baby will not "tell" you their diaper is wet or soiled.
Just some ideas and thoughts.
All the best,
Susan