True, it doesn't make much sense that the refitted Enterprise had the exact same weak spots, but that's the official explanation.
Khan caught the Enterprise by surprise, and knew exactly how to do the most damage. It was the initial attack that crippled the Enterprise and gave the Reliant a tactical advantage. The only advantage Kirk had in terms of experience was that Khan was thinking as a 20th century naval commander, and wasn't really taking advantage of the all three dimensions. If she hadn't gotten those first free shots and hadn't been commanded by a genius, I don't think the Reliant would have stood a chance against the Enterprise.
I don't have any SFB material on hand, but SFC is based upon SFB, so I doubt there is a great deal of difference. SFB is not cannon according to Paramount. After all, on screen, Klingon ships are armed with torpedoes and disruptors, yet in SFC, they only have two disruptors and several phasers. On screen, nobody uses missiles, unless you count photon torpedoes which can be seeking weapons, yet SFB has lots of stats relating to drones. SFB is a separate universe from cannon Star Trek as seen on screen, and not cannon, at least according to Paramount. Or put another way, cannon Star Trek and cannon SFB are two different things. SFC is based on SFB, not the cannon universe, so if you want to make SFC look more like the movies and series, SFB won't be much help. Now, being a pnp game, I'm sure there are lots of custom stats which describe the Reliant's phaser pods. With a little research with Google, I'm sure you can find all sorts of custom SFB style specifications for the Miranda class that you could use, or at least give you some ideas. Like I said before, your best bet is probably to just work out your own stats that make you happy. If I had to choose mega-phasers for the Miranda, my first choice would probably be PhX, since the damage seen in the movie isn't really that terrible, given the circumstances. My second choice would be one Ph4 on each mount, with a small arc. I would leave the power alone. A third choice would be PhA or B, with a small increase to the power. B makes more sense in terms of damage, but A looks more like the SFX in the film.
OT: Don, I can?t help but ask, is your avatar wearing any pants?