Well, cores aren't THAT hard to farm, but it could be an annoyance, yeah. On a side note, Tri-Tach took over one of my Alpha Core governed colonies, and they now have a colony with an Alpha Core governing it. This one makes sense, tho, since it's Tri-Tach, after all.
I hadn't seen Boggled's mod before, it's not that. It's the handmade sector, and it's not a system added by any mod, as far as I know.
I think originally it was one of the colonies formed by a tri-tach expedition, the colony got decivilized, most likely, while building the orbital station. The second spaceport never ended up being built, it disappeared. The phantom station kept being there until I started building a real orbital station to replace it.
Edit: Is there any way to tweak blueprint drops from raids? It's gotten a tad ridiculous, fighting a star fortress and then wasting tons of fuel on bordbardment, only to get a blueprint for a weapon, and a lot of the time these are already known. So far, exploration has been way more valuable in obtaining blueprints. I've literally not once seen a capital bp drop from raids, cruisers, tops.