Lyraeus your OCD-like attention to detail is normally great. It's from a lot of your posts that I've learned to step back from what I think upgrade cards say and look at what the cards literally say. I don't know what part of this is bothering you, maybe just the fact that the fire control teams circumvents the original one critical effect per attack rule. FFG has made it clear for a long time that none of the rules are immune to being modified by upgrade cards. This is kind of a little slice of hell for rules lawyers, but it's the way Armada is being written. I use the current tense because I'd be willing to bet that they're planning rules bridging upgrades for future waves.
At least for me, I had to step back and look at how Fire Control Teams rewrites the phase steps for ships that have it. I look at what the card says without reading into it and it seems that all this cars does is exhaust to allow a second critical effect. I know if seen the attack order described by you before, defense tokens declared in defense token phase even though only scatter and evade take place then. All crit effects are resolved in crit phase, even though some are applied with damage. Total hits and Crit symbols added up for total damage from that attack. Just because a critical effect isn't applied until the damage phase, doesn't mean you lump it in with the "normal" damage from the attack