Basically, the same green spirit bomb that spawned for Yamato v1 can spawn twice in v2. Also, naturally, the v2 bomb hits harder. Maybe the second bomb took your MPA by surprise.
I don't think the commander has to be alive for it to spawn a second time. I could have sworn that I was in an MPA that took him down quickly, but the second bomb still showed up. The commander is just usually still alive since he has more health in v2 and because of the extra chaos during that part.
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