I can actually totally respond to this question without revealing secret info, yay!
(NOTE: THE FOLLOWING BELOW IS MY OWN PERSONAL EXPERIENCE AND DOES NOT IN ANYWAY REPRESENT THE VIEWS OF KONAMI DIGITAL ENTERTAINMENT, PARTNERS OR OTHER)
You have to think of it from both a business and technical standpoint. Usually, putting additional content onto an already-printed SKU requires that SKU to be reclassified and resubmitted (now that the content on disk is different than the vanilla product it is technically a "new" game), which has additional costs and additional time associated with it. Some of the new changes would require additional copies of the game to be printed with new box-art, reclassified, go through rigorous testing, additional legal, creative (packaging, manual), have a new listing on Digital Storefront, negotiate with retailers for shelf space, etc. That's a lot of money and manpower!
If a game/book/movie is really, REALLY popular and already sold through a bundle (like I assume it was for Batman: Arkham City), then it's totally worth it, and can bring in new revenue. So re-issuing new copies becomes a cost/benefit analysis of "what can we afford to do in a re-print?" In most cases it would be a new box, maybe some new creative, but the priciest option is putting additional content onto the disk.
As a general rule of thumb, if you have to ask why company X would do Y action, it almost always falls back to "would not be sufficiently profitable" and what I've said applies to just about any creative work, including games, movies, books and music. That's why many have opted for digital downloads, which is a remarkably cheap and easy way to do it.
Whew! I think that was sufficiently platform/company/industry neutral to not raise any ire.