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It doesn't really matter which is the base and which isn't. The actual operation is an AND, which is order independent.
In particular you would be able to use virtual libraries without using restrictions and vice versa. The question really is whether virtual libraries need to have the same set of persistence features as restrictions, namely, specifying a VL at startup, and perhaps for the content server as well.
Certainly, I imagine VL will become the primary way to use search restrictions in calibre. The restrict to dropdown will only be used when an additional level of restriction is needed.
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