SlickRCBD
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That seems like an extremely stupid way to do things.It was an unintended side effect. In that timeline, Coil started going through the PRT databases, which allowed the virus to invite more malware into his base computer. Thus increased in complexity, it started mapping out his computer system in detail and digging into secure corners. Coil being a paranoid bastard, he had a setup where unauthorised access to his computer set off the self-destruct. The virus accidentally triggered this, because Dragon didn't think to safeguard against that level of Bond villain paranoia. Boom.
Having a self-destruct for the computer for unauthorized remote access would make perfect sense. Blowing the whole base should only be done if the base defenses are physically breached.
Also IDS systems are prone to false positives, hence why you would want to limit the automated self-destruct to the computer alone.