As you noted, copyright does not protect ideas. Copyright protects the expression of an idea, that is, the exact words (and/or pictures and/or sounds) used to express an idea. As long as you write a description of the setting in your own words, you are not violating the original author's copyright.
A setting such as this example is an idea and cannot be copyrighted. (Again, along as you describe it in your own words.) The "setting" here really isn't a place per se but the idea of a collection of books meeting certain characteristics. An author cannot "own" such an idea. New writers on this and similar forums often worry about such scenarios: "I am writing a book where a young man and woman fall in love but their parents object and try to prevent them from getting married, and then I came across this other book that's also about a young man and women who fall in love but their parents object and try to prevent them from getting married. Am I accidentally violating copyright?" No, you're not. Copyright does not protect general ideas, only the specific expression of those ideas.
From a creative point of view, I'd advise against copying another writer's idea too closely. Readers will think you are unoriginal and unimaginative. Better to be inspired by another writer's ideas: Take his idea, but change it enough to make it truly yours. In this case you could easily take the essential idea -- a collection of all possible books of a given length -- and throw out the part about hexagonal rooms, change the number of pages, etc.