The titles you see on store shelves were not done with a tools like Encore or DVDit Pro. Apps like Blu Print and Scenarist 4 were used to create these titles. I believe Panasonic has a tool but it's not sold to the public. There are 2 types of BD authoring: HDMV and BD-J. HDMV can be similar to spec authoring in SD DVD in some ways. There are pre and post commands for example. I've done both HDMV and Advanced HD DVD titles and, beleive me, HDMV is MUCH easier! :)
BD-J is where Java comes into play from the operator's POV. A BD-J object takes full control of the player's playback functions while having pixel by pixel control. A complete grasp of object-oriented coding is a must. The problem with BD-J, IMO, are the costs and time it takes to code these titles...at least at this point. By the end of the year you might see affordable BD authoring tools. I know the guys at Net Blender are working on a tool.
The costs for replication can vary wildly. For 2500 units, I've seen quotes from $2500 - $6000. Then there are the AACS license fees which will set you back another 3K or so. I don't have an exact number yet for I'm in the middle of replicating my first set of titles.
The BD spec is complete. Folks often get confused on this. It's the player which don't support the entire spec.