Note one thing: BWO aims to follow on Freespace's style and tone. One of the things about FS1, ST and FS2 is that there are always more than one enemy at any given time, and those plots are always connected in some way. Some might seem disconnected at first (the NTF for example, until Bosch's real agenda is revealed), but they definitely play pivotal roles in the larger issue, or exist as a consequence of it (HOL).
BWO does the same. Superficially, one might interpret that the Vasudans are extremely unified as a species, that Khonsu is adored by all, but that's not true at all. The SoV is a lens into the opposing perspective.