Yes. But we are comparing apples and oranges here...
I am not sure, but your search, as described in the screen dump above, when used in a VL, seems to be the equivalent of:
not (tags:"=Apples" and tags:"=Oranges")
It would match any book that didn't contain BOTH Apples and Oranges.
The search made by the OP was:
not tag:"=Apples" and not tag:"=Oranges" which can be rewritten as:
not(tag:"=Apples" or tag:"=Oranges")
(De Morgan's law)
It would match any book that doesn't contain either Apples or Oranges or both.
See De Morgan's Law:
A OR B = NOT ( NOT A AND NOT B )
...and that is the same as:
NOT ( A OR B ) = NOT A AND NOT B
... that I used above.
And the latter result is indeed what Calibre seems to give when used in a VL.
Example: a book has tags: Apples,Oranges,Peaches,Pears.
The search "not tag:"=Apples" and not tag:"=Oranges"" would NOT return that book, because it contains both Apples and Oranges. (If only one of Apples, Oranges had been present, the result would have been the same.)
(I hope I got this right, it was some time ago I read boolean algebra and I got a headache from this...)