Well, recharge rate is also listed in the playtesters' guide, and it makes sense for them to be two separate stats. There really has to be a gun capacity stat, even if Armedit doesn't support it, because after all - if the Arrow with its two lasers had the same gun capacity as the Banshee or Goran, then either the Arrow would take forever to run out of energy, or the Banshee would run out of energy in one salvo.
I'm not surprised by your findings regarding manoeuvrability - I got the impression from the playtesters' guide that this change must have been implemented somewhat earlier than the gun changes, because of the way the guide seems to avoid talking about manoeuvrability altogether. It makes two offhanded remarks about the Arrow being highly manoeuvrable and the Banshee not being so, but even then, it seems to connect manoeuvrability with speed. So yeah, it makes sense that the game will be hard to play with the manual values. Same for the AI. That's a bit of a pity... but then again, it really isn't. Armada is Armada. It's a weird, hard to play and sometimes kind of unplayable game, but the speeds and the jetfighter-like combat are precisely what gives it character. That having been said, I would love to see Armada's fighter fleet imported into WCP, with the manual values for manoeuvrability. It would be quite a different experience.