No secret compartments, but I've found it's easy to attach bungee to both the top and bottom of the Mod Pod for holding tools and lure boxes. And Like Jim said it's more rigid so you don't have to worry about it buckling if you sit on it.
My only small complaint is that the Scotty style rod holders don't lock. Although they are plenty snug.
This video details all the features of the Mod Pod:
http://www.youtube.com/watch?v=dwxWufm7fCI