I have done some investigation, and I cannot find any easily accessible way to define, or re-define, the special structure regions that vanilla adds (as nbt in .dat files). This would be invaluable, as special mobs like Guardians and Wither Skeletons can only spawn in such places.
It may be possible to fake something using WorldGuard etc, when it’s available for sponge. But what I’m talking about is actually messing about with (or substituting) the data from the .dat files in Minecraft world save files. There may also be practical benefits to setting the StrongHold and Village regions too.
I’m not even sure if it would be possible with the current SpongeAPI. It just seems to be something nifty to mess with, and I have seen a great many questions on the topic elsewhere, with no satisfying answers.
If anyone has any clue how to make something that could perform this task, please let me know.