For your first question: Yes, there is a physical reason for this phenomenon as is (or should be) for every observable phenomenon.
For your second part: Depends on who is debating the validity or applicability of that theorem. Can you please add a reference, then perhaps someone may be able to answer it.
For your third question:
Yes there is a lot of "real" dynamics involved here. In fact, because a lot of objects are interacting with each other, it is highly involved as well. Different models to explain/simulate flocking behavior use almost the same physical phenomena in their calculations --gravitational pull from earth, fluid mechanics, wing flapping. What they debate is usually one or more of the following:
- What is a bird's comfort level of independence? Meaning, how far will a bird on the edge will go away from the flock before it senses danger. This has nothing* to do with physics and has everything to do with such factors as the predators around, the evolutionary history of the birds, etc.
- How close do birds like flying to each other? At what distance they sense an impending collision? Again, nothing to do with physics really.
- How perfectly do birds prefer to align to the group? Is there a single leader or multiple?
- Does a change in the wind's direction change the leader's course?
One can of course abstract out the biology and social behaviour out of this model and empirically define a force and construct laws (similar to Newton's laws of gravity, Maxwell's equations etc.) for that force. Perhaps then that person may be able to reuse some of the results that physicists have derived for other problems (note: this depends a lot on how your force laws are defined). Basic physical laws that apply universally shall still be applicable.
*You can say everything is physics deep deep down but that is not the point here obviously.