You seem to be missing an important detail in this process.
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The fundamental problem is caused by the operator, not the software. To reverse the order, when you have a stack of papers, is a well understood process
Not so I beg to differ - and here's why: page reordering is a basic reprographic function and it doesn't matter how one comes into possession of said documents (PDF or otherwise for that matter), it is only fair & reasonable to expect this function as standard anyway i.e. they may not have even done the original scanning themselves.
... or can be re-derived with some very simple experiments: Take the top sheet from the source stack and place it as the bottom sheet of the destination stack. Repeat until the source stack is exhausted. Now scan the re-ordered stack.
Yes you are correct to say this but only to a point. Whilst the user could, perhaps, perform a 2nd or 3rd pass to get the reordering correct, that would seem again, fairly redundant given the facilities meant to be offered by any system in general, but especially by Apple (bearing in mind previous postings other than my own).
Besides, if a lot of work is involved (like mine was - and it wasn't even a professional task) then expecting the user to take a multi-pass approach to a service that is easily rendered in software - and indeed should be - is again, a waste of time. It is akin to taking a taxi cab to drive you somewhere, paying full fare, and then being told 1/2 mile from destination that you'll have to finish the drive yourself.
Admittedly, the scanner drivers ought to provide this feature also, as part of a discrete package but all the same, the Apple brand has to mean something too and so it follows that once in PDF, ODF (or whatever) then it doesn't matter what the source was, the ability to reorder should be present and obviously so at that (again, like other features Apple sells it's image on).
So yes, the user could have been able to avert the problem but they are still NOT in error here as s/he has every reasonable expectation for their method to work as a valid one (and is in my opinion a superior because of it's efficiency).