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The "black box" concept wasn't mine originally; unfortunately, I can't think of who I stole it from. They deserve the credit.
Something else to remember: drive space is CHEAP. I saw an external 1 terabyte drive at Target for $79.95, take it home and plug it in. Eighty bucks a terabyte, off the shelf. If your library occupies, let's say, a gigabyte of space, and calibre imports the books, taking another gigabyte, calibre's copy of the books is costing you eight cents.
So, if you really need to have copies of your PDFs along with something else, and they have to be separate from calibre's copies -- that is, a link to the file and calibre's viewer wouldn't suffice -- it's 8 cents a gigabyte to keep them there. I'm pretty sure most of us can afford that.
I'm pretty sure calibre won't be changing. It does what it does very, very well; you could even say "right and perfect". There would be no sense in regressing to doing that not-so-well so that a small minority of people could use their computer's filesystem to sort-of store metadata, given that pretty much the whole point of calibre is to use its own, much more detailed, metadata. That's rather like saying that a file manager should provide physical disc access instead of dealing with files.
And, as I always say, read my .sig.
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