Yes this is intrusting hmmmmmmmmmmmmmmmmmmmm
Just finished the final mission and came to see if anyone else wondered what it was all supposed to mean.
One thing I can add: The explosion does NOT destroy the base. It only destroys the entrance. If you drop a radio inside the base before you complete it, you can go back inside and the computer is still intact, no damage at all, the whole base is intact, but the entrance is caved in. I thought I might run into some horrible robot and die, so I dropped one, and after the credits I was able to go back in and look all around, pick up loot that Iād skipped, etc.
The FOA bunker is meant to be destroyed completely story-wise, but it proves too late to stop FNIX from spreading, since the Machines are still roaming around after you blow the EMP.
If you thought that because it seemed a bit weak, donāt worry, you got it, it was just a bit weak.
Just in case though, TVTropes unsurprisingly has an interpretation.
You know, here in Sweden we donāt call them āRussiansā. The army and the navy call them ābeaversā or āsealsā when their submarines come a bit to close 
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My idea was that Dr ulmar transferred his mind into the super computer and due to his hiv or aids his mind went mad in the super computer and the Russians install a virus into the main frame thatās what that briefcase was and he was killing people and taking their bodies to the lab to transfer their mind into the computer system and control the machines thatās why u see very few bodies in the towns and cities
what you said makes a lot of sense what i noticed is that on the screens from the entrance to the laboratory you can see a lot of corpses in a sack and exactly when you come in finx turns off the screens
Read ingrids resignation letter explains alot