I like to think there is a bit more back story on Team Plasma, as I don't think they were focused on a lot. I mean seriously, it was more like a Civilisation than just a team. There was so much more of that put into it all, I mean, they have sages, and a King, including goddesses (Anthea and Concordia) I think somehow maybe they managed to teleport it there or something like that, using some Pokémons power. It was probably build 200 years ago for all we know.
Either something along those lines, or those big white planks (or whatever they are) infront of the castle in the opening is what hid them. xD