How do you pick which enchantment you want? If you put 3 enchantments on one item, you cannot repair that item easily. Since all of these are higher ranked enchantments, it is not feasible to repair the item. After the item wears down, you would just toss it. I'm sorry, but this seems to be either very dumb, or very flawed. Why not just put one higher ranked enchantment on a book, or make a book where you can choose an enchantment that it will have?
Alive and kicking in the 1.7.2 release...
Dinnerbone was kind enough to go out of his way and clarify the issue for me:
"If you have a book with 3 different types of enchants on an item, only valid ones will go through and you don't pay penalties."
Thanks Dinnerbone, and hope this helps any others who did not understand this.