You know, my playthroughs of the game literally number in the triple digits and I never, ever thought to blow the console up with explosives.
Really, I can't think of any logical reason for this to happen. The best justifications I can come up with are incredibly flimsy ones, and regardless, they'd all be invalidated by the fact that any forensic evidence that could've established how the deed was done would remain buried beneath thousands of tons of rubble until The Enclave dug it out a few decades later. A bit of logical analysis seems to suggest that there's no direct-line communication between the Military Base and the Cathedral, and the psychic link established by The Unity doesn't seem to be of a nature that would allow for unambiguous communication of higher-order thoughts over long distances, so to the Master and the mutants, the Vats would just be a big heap of mysterious rubble one way or the other.
In short, wtf? I haven't seen the code (and if I had, it would be gibberish to me), but if I had to take a quasi-educated guess, it would be that it was a programming oversight. It's possible that the invasion-halfing was meant to take place however you blow up the Vats but they didn't link it to the self-destruct method, or that they started to implement the feature, decided against it before it was finished, and forgot to undo what was already in place.
