(Interesting build, but unfortunately no plot resolution)

Aside from the issue they mention of "the enormous backblast" the ceiling they refer to as "very easy to remove" seems like the kind of "easy" where it only requires a cherry picker and bunch of labourers working for hours opening it up for a crane, which is not exactly rapid response. Plus it would be even less effort to put the missiles on a roof somewhere else.

I think the explanation is the simple one in the article, they wanted to put heavy stuff there by crane which would suit loads of industrial equipment, as would the extra thick floor. While the article posits these things would "exit the building on its own" it's probably even more likely they would exit the same way they got there, by crane.