I see what you mean, and I think I know why this particular section of scientific intrigue is so controversial. It's because this field of science, more than most others, is always changing, sometimes fundamentally, and so you're left with various schools and denominations of the same principle. In other branches of science, philosophy has already become an integral tool in the realization of the implications.
For instance, think about evolution. Though you have different levels of evolution (micro, macro, etc...) the principle is always the same. The general philosophy follows that creatures have gradually changed to what we have today, and are continuing to change. Though the evolution of bacteria may be different than that of macro-organisms, evolution is evolution, and they're all complimentary.
If you look at physics, though, you find a canyon between the two schools of thought, relativity and QM, and they are fundamentally incompatible. In such a case, the philosophy won't be clear, as is evident here, because there is an obvious conflict, and both sides will have a difference in their universal philisophy. Of course, this implies that there is still a unifying theory out there which will combine the two, and then a general philosophy can be gained from this. In reality, this will be one of the most important findings in the history of man-kind, right up there with relativity and evolution, and once it has been discovered, you can bet that everything about current philosophy will change, since the implications are found within all branches of science and reality. I'm really hoping they find the solution sometime in my life time
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