@The Pentacle Queen,
Whilst writing my dissertation (it was a musicological essay) I was consistently irritated by reading article after article that dealt with my issue by literally making massive webs of argument that superimposed meanings onto the subject making convincing reading at a superficial level, but when studied closely, held only tenuous links to the object of study.
In this case, my argument was that the theory was not servicing the work, but creating systems of meaning to service itself, which in most people's books I think is bad academia. I would like to posit that 'better/good' academia would hold a more cogent relationship to the object of study, and not create long chains of argument as scaffolding, not thrust meaning 'onto' a topic. However, in 'better' academic studies, I don't know if we can make a proper distinction between whether theory creates or extracts meaning, since creation and extraction have the same appearance. My guess, of course, is that it does both, but I can't work out exactly how.
I think there are two processes going on in what you've observed. One is simple academic claim-staking: arguing a theory (or perhaps more accurately, a thesis) as a career move, something to provide fodder for the publish-or-perish machine. Given enough time and research grants, one can string together almost anything out of the available material - to "prove," for example, that Bach's Tocatta and Fugue in D Minor is really a blow-by-blow representation of an argument the composer had with his wife over the grocery money.
The other process, the one with philsophical resonances, has to do with the fact that our perceiving or thinking about anything involves a selection process. Abstraction is one name for it, reductionism is another. In my opinion, we can and do experience things as wholes, but when it comes to "thinking" about the things we experience, we can only think part of what we've experienced. It's why the breaking down of a process works scientifically, but it's also why science often ends up having to deal with the ill effects of what it has overlooked.
It's also why, as individuals, if we have any sensitivity, we return to our experiences again and again and think (or re-think, re-cognize) a different part each time; for example, listening to the chorale in Beethoven's Ninth Symphony for the hundredth time and still hearing or feeling something new in it. And my hearing or feeling that new strain might prompt me to invent a new theory about music, about aesthetics, about life. So it goes.