I don't think it's wrong to take backstory into account. It's one factor among multiple factors. Realism is good. Having intuitive mechanics is good (intuitive meaning that someone who knows nothing about the game itself would assume that it's supposed to be that way--like the fact that a unit named a "bomber" is a plane that drops bombs, or that bigger tanks beat small tanks in a fight). Modeling every projectile is good. Units being responsive to orders is good. Those are all things that are generally good, and are generally supported in the game, but we compromise on all them in various ways because you can't have everything. Having good gameplay is the most important thing, but it's not the only thing.
If we only ever asked "what tweaks can we make right now to make the game a little bit more balanced/interesting" without worrying about those other factors, the game would become really bad, really fast. Probably every unit would have toggleable abilities like the Loyalists or like Overcharge to reward APM. We might cap the amount that you're allowed to zoom out because it makes the game more fast-paced. We could drop the unit count, make units bigger so they have flashier graphics, and add global upgrades so that players have to commit more to a particular type of tech. Basically make it more like StarCraft 2 and Supreme Commander 2.
That could be a fun game, but it wouldn't be FAF. Preserving the unique identity of FAF might be equally important to "Having a well balanced game with interesting features."