What is the physical basis behind the independence assumption in Bell's theorem? Bell's theorem rests on two main assumptions: locality and independence. Locality has its basis in relativity and it seem to be a property of all known physical theories accepted today (General relativity and the quantum field theory).
The independence assumption (also known as "freedom", "free-will", "no-conspiracy") implies that the hidden variables and the measurement settings are independent variables. This seems intuitively appealing, but is there any reason to accept this assumption?
The modern theories I mentioned above are field theories. In such theories the state of a subsystem is not independent of the state of the entire system. Stars in a galaxy do not move independently of other stars, charged particles do not move independently of other charges even if the distance separating them is large. But the source of the entangled particles and the detectors are nothing but such subsystems of the whole experimental setup.  They are nothing more than large groups of charged particles (electrons and nuclei/quarks). So, it seems to me, that the independence assumption is in fact contradicted, not supported by the mainstream physical theories.
 A: Experimental science is based on the idea that what you measure is independent from your measuring device. Or at the very least that it is not a part of the measuring device.
What can you make of any experimental result if each experiment is taken to be a specific expression of the whole (aka the universe), without any sensible division between an observed system and a measuring system? 
Without that independence assumption, there is no science. And since researchers over the ages actually did find more or less valid laws of physics, through uncountable experiments, such independence somehow holds. Rejecting it would immediately raise the question of why do experiments actually yield results from which one can infer generic laws and principle governing the behavior of (sub)systems?
It is for good reasons that explaining away the violation of Bell's inequalities by giving up this principle is seen as a "conspiracy theory": it would mean that while the universe appears to follow specific patterns implying the separation of systems, everything is actually connected together in the background so tightly that all that happens is strictly predetermined (one then talks of superdeterminism). 
Now perhaps the true nature of things is beyond these distinctions, as in this zen quote:

The blue mountain is the father of the white cloud. The white cloud is
  the son of the blue mountain. All day long they depend on each other,
  without becoming dependent on each other. The white cloud is always
  the white cloud. The blue mountain is always the blue mountain.

But is this what physics is about?
