Yes, we're aiming to have all ships default configured as close as possible to what they're 'supposed' to be. We've covered the list of where we want to grab this info from many times in the past, as you've stated you've seen. The fact is, Lucas envisioned the combat as WWII in space. So, the fighters fly like fighter planes roughly, fairly low agility, but moving relatively fast. The capital ships are mostly designed to either launch fighters, attack other capital ships, or both. Fighters will play a role against them, but will have a very hard time singlehandedly eliminating any but the smallest capital ships. This is fairly close to how fighters were used in WWII, swarms of them could inflict serious damage, but only when used appropriately, and it would help much more to have some capital ships of your own aiding in dishing out some damage. We hope to avoid using mechanics and such that were only seen in the games, because we're not trying to recreate the old games. We want to make something new, that feels different wherever necessary to achieve a slightly more realistic, but still fun, feeling.
And as far as complaints that having all that firepower on the capital ships will be hard to balance, just because ships can carry X amount of guns doesn't mean they'll always be configured that way. The mission designer can rearrange or disable the turrets however he wishes within the bounds of the table, which won't be very restricting. I just see no reason not to allow the maximum level of firepower possible, for when it _is_ wanted.