Presumably when they stop reading Book A after the 5% mark, they would move on to Book B and Amazon will then pay the author of book B. So Amazon is paying someone for the whole duration that the customer is reading from their collection.
Personally I think it's a fair arrangement. Some of the "books" are really low effort cash grab that you'd literally open, read 3 pages and drop - it'd be unfair if they got paid just as much as well written works of the same length that you finish reading through.