Free feeding vs scheduled feedings I believe depends on the individual dog, what works best for them. I sort of free fed Max his first year. He ate a set amount of kibble throughout the day. Now we do scheduled feedings because my boys would eat an entire bag of food if I left it out for them.
I do not believe that free feeding will cause any behavioral issues.
Regarding the alpha theory, I think it is a matter of semantics. The humans are definitely the leaders in my home. We don't believe in demonstrations of domination of the dogs, but we are in charge.