Miss Information brings up an interesting question about the Iron Five. Given her origin I have to assume that she’d hate villainous versions of the FF as much as the heroes, maybe even more so. Might be willing to work with them for a while to ruin the heroes’ day, but eventually she’d turn on them, maybe even taking over their organization if she succeeded. Luring them and an iteration of the heroic FF into a mutual deathtrap would be a win-win for her.
In all honesty, I rather like the idea of hovering penthouse sphere/mobile command module/team spaceship over a more conventional skyscraper HQ. Seems like the kind of thing Reed Richards would build, zoning and FAA laws be damned. Still less intimidating than the Sentry’s digs, cloaked or not.