Its not really clear what config setting are library specific and what are not.
For instance hidden columns: I'm sure there are people (I'm one of them) that dont care who the publisher of a book is and so want that column hidden in every library.
Or saved searches: I may use saved searches to find the newer books, unread books, etc that would be common across libraries.
As it is, with the current setup of sharing those config values, as long as you are careful to have the same set of custom columns in each library, there should be no problem.
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