Not many that I have found. If a company is going to do a bundle, it is usually a little different quality or blend with different branding. RomaCraft, San Lotano, Island Jim #2, and some others offer bundles of their regular line boxed cigars at a lower price.
Sometimes seconds, as you mentioned, are offered by some companies. They could be re-branded to not dilute the main line reputation. Nude bundles are a good example of little to no branding and a lower price. The bundle could be made by a major, brand-name company.
Price difference with the box is around $5, so add retailer mark-up on that, which varies. The thick solid wood boxes that RoMa Craft uses could be much more with a higher cost to ship to us and to ship to you. Most companies want to keep the whole marketing package together for their regular lines. Padron is never going to sell a bundle of Anniversarios (unless hell freezes over).