I'll post this here even if Coby answered elsewhere, in case my phrasing is more helpful to someone different:
You can create your own separate sprite sheet and associated XML and include it in the game. The formatting of the XML will need to match what Texture Packer spits out, so you could look at bulk_01.xml as an example. Remember there are two PNGs and XML files for each sheet, one for HD and one for SD.
Once you've created a new sheet, there is a file in the /art/textures/ folder called texture_list.xml; this is where you add a reference to your new texture. Assuming everything lines up with the XML, it will be read in correctly when the game loads and whatever is used for the "n" attribute for each <sprite> reference in the XML will be the ID that can be used in the JSON files, the CSVs, etc.
There is no limit to the number of textures that can be used, but obviously the more you have the more of a performance hit the game will take.
Regarding the enemy behavior sample, we're moving toward something like that. This will mean that I can define the enemy behaviors without needing Coby to compile so I can test and blah blah blah and also exposes that data for modding down the road. In general, whatever is good/easier for me to use is good/easier for everyone else; I am our prototypical modder.