It's not clear how The Fantom passes through the ground. On this page, it appears he can become intangible. On the next page, it says he went through a trapdoor that we never saw him open. Maybe it's some sort of revolving trap door that you just have to land on a certain way to make rotate...
In my campaign, the group is based out of Los Angeles instead of Glasgow, and is strictly limited to U.S. interests instead of global missions. I could see a campaign where Heroes hop from organization to organization like this, moving up to a bigger organization as they go up in level.
Now, meta-gaming wise, this is actually poor playing because they may not get any experience points for defeating the mobsters, and they'll loose any xp from claiming trophies from the hideout since they burned the buildings down before looting them. With this style of play, though, the Editor serves the players better by awarding one big xp award for an accomplished mission, rather than for the details of the mission.
(Scans courtesy of Digital Comic Museum)