Just because something is explained doesn't make it believable. I have to agree on both points actually. Watching one of your wingmen tear straight through the sentry field and corvette screen in Her Finest Hour with the AWACs/Auroras active looks absolutely ridiculous. I was able to say "well, ok, it's just a game", but suspension of disbelief failed for a moment there.
Here are a few fun alternatives, though:
1) Your wingmen aren't guardianed, you lose the mission every time they die
2) Your wingmen get protected when their weapons subsystems are disabled; enemies magically stop shooting them
3) Your wingmen jump out when they're badly damaged; every line of wingman dialogue in the mission from then on needs to be treed, and the player can be forced into mission states where they have few available tools left
The Custos is slightly more believable because it basically handled like a fighter, or, well, like a Uriel with turrets. But then you go up against a destroyer, two gunships, and several squadrons of fighters and wreck them without really being threatened, and on a time limit. I suppose others had more difficulty than I did on this mission though. If soloing that kind of threat while outgunned isn't Alpha One syndrome, I don't know what is.
If taking on a fringe society's several-decade-old converted transport and light, obsolete fighter support in a top-of-the-line littoral combatant purpose-built for the mission feels like Alpha One Syndrome rather than Doing Your Job then I don't know what Alpha One Syndrome means any more.