That picture was not meant to represent the entirety of the library, but rather, some of the side rooms of it. The main portions of the library are perfectly tidy, and that's where most of the books that the Initiative considers most important and most likely to be of interest to the transports. However, the Initiative has been preserving any books they can find, which means they have centuries worth of books and don't have enough manpower to keep everything perfectly organized. So if characters are curious enough, they could find hidden-away side rooms like the one pictured, filled with the thousands of books that they don't consider important enough to have taken the time to organize yet (such as piles upon piles of 20th century Harlequin romance novels and copies of The Complete Idiot's Guide to Windows '95). If a character wanted to take it upon themselves to organize the contents of these storage rooms, they would be certainly welcome to do so.