I think you should follow the directions - they are there for a reason.
You can enable the checkbox when adding other media, but when adding books, you need to disable the checkbox. Why? The simple answer is that when calibre makes changes to a book, only the copy in calibre's database is current. If iTunes stores a copy, it's a snapshot of the book at that moment, and any subsequent changes you make in calibre won't be made to iTunes' copy. There are other deeper technical reasons for this recommendation as well, but that's the simple one.
Keep in mind that you are actually using two database managers to send books to your iPad: iTunes and calibre. Managing that checkbox is one of the necessary compromises.
G