The problem is, the method used for custom vcd fles at the moment means that they require the creation of the file scenes.image, which must be placed in the scenes folder.
You can't, for example, make a scenes2.image file, and get the game to see it. This means that any custom scene files have to be named in a way that overwrites the original, and since they can't be embedded in the bsp, there is no way to use them without breaking the original game, or making a mod.
This is the situation with the beta sdk, and so, has a good chance of being the same in the release, since I haven't seen anyone complaining to Valve about this method yet.
Also, I don't think that bmz files will solve this, as they basically just extract the files to the correct folders anyway
It is also worth saying that there are other files that will not work when bspzipped. Some of the script files are executed before the map loads, and so modified versions packed inside the bsp will not function.
I may be wrong about some of the above, so feel free to correct me. That is just my understanding of it. Also, I would love to see some evidence that Valve will be making custom scene usage any better than it is in the current beta SDK implementation.