“I'm not sure how we're supposed to balance anything if everything is just aligned to canon? ”
Through the equations and skill weights, to some degree (which I really don't think are even close to their final form given some of the differences between prior combat discussions and current implementation), but we also have leeway with shields and maneuverability since those are ambiguous factors whereas the specific weapon configurations usually aren't (and I suppose our travel speed values have for many, many ships never
resembled canon so I don't really expect that to change).
In theory there's also the option to use something that works like firepower currently does for weapons, since that's just SWC-specific and doesn't actually require ships to have their known configurations completely ignored. But ultimately some ships are obviously going to be better or worse than other ships, or better or worse for specific purposes and circumstances, which is okay. Some of that is simply balanced by the production cost of the ship.
Part of the issue, too, is that making changes that actually move ships farther from their canon specifications right now doesn't make any sense until combat itself is closer to its final implementation.