There are several different parts to this thread, I will try to address the different parts.
The OP asked about a batter not being in the box completely and the pitcher pitching. This is a balk in either OBR or FED. It is odd the BU called this. The PU usually calls this which is why I asked about the PU having his hand up.
Then the batter stepping out was brought up. If the batter does something that causes the pitcher to stop then it's a do over. This is true in both OBR and FED.
The balk rules are a little different between OBR and FED but without going back and rereading both codes, I believe everything that is a balk in OBR is one in FED but FED has a few additional ones thrown in.
The deal with OBR being used at different age levels is another story. In some organizations,LL and CR come to mind, disallow balks below a certain age. CR and Pony have a couple of option ages where you can or can't depending on how you set your league up. If you are working a system that has balks at 9/10 or 11/12, then the rules are same as in pros. How particular you are will depend on age. What I am saying is you have to call the elephant balks no matter the age. But the more technical balks are either call loosely or ignored.