Larian doesn't seem to care about the story, or at least doesn't seem to care about the story enough for a game at this scale.
The argument you present (i.e flags) in defense of this statement does not stand. Some oddities here and there does not override everything else about the story, nor show that they don't care.
As for the flags themselves, there are certainly some odd things afoot at time, but it is EA. So, at the very least, this argument is premature.
