SPS nailed it - the box does a horrible job explaining the point. It's funny they don't show the most popular layout of all -- 1/3 offset. You can use whatever pattern you desire. You might or might not notice the lippage. You can always use a good tile leveling system if lippage is a concern. It probably won't fix heavily warped tiles, but that is something you can check in the store if you're buying from Home Depot or Lowes. If you've got heavily warped tiles you're going to have a problem no matter what pattern you use.
Wood plank tile: it's beautiful and offers so many advantages over hardwood floors. What kind of grout joint offsets should you work with?