Ok, here is a possible lore friendly way to inject them in.
While the Madre and the construction company were used as lab rats and testing ground respectively I feel that the Scientists of Big Mountain, being men and women of ~SCIENCE!~, would run more than one instance of the experiment at a time. You know, multiple data sets, a control group and all that. Can't have unconfirmed information, that's unscientific! So there would be a new location, maybe an unfinished railway tunnel that was in mid construction, that was also being used as a test.
When the bombs dropped, it collapses the main entryway in and trapped the workers inside, protecting the commonwealth and capital wasteland from the menace that would eventually be called the Ghost People. But there could be something down there that you need to get and you need to breach into the tunnel and when you breach it, you actually do it violently and irreparably. You clear the location, kill all the Ghost People
and get the objective but this place... it's littered with (unreachable) cat walks, blockaded access tunnels, broken/empty elevator shafts and big busted pipe work... going deep into the earth of the commonwealth... and its filled to the brim with unknowable amounts of Ghost People. From then on the Ghost People are free to escape the underground and run amok in roving packs across the commonwealth.
Well, whatcha think?