When examining the meaning of fantasy literature, such as "The Darkness That Came Before," by R. Scott Bakker, one has to first overcome a significant problem with the genre as a whole -- it's relationship to history.
Fantasy, as it's often written and enjoyed, is meant as escapism. Fantasy literature often plucks the most romantic and dramatic elements of the popular conception of European medievalism, adds a dash of magic and monsters, to erect the vague skene in front of which the traditional stories of disguised princes, princesses in peril, and wandering wise men appear. A reader goes to this world with idea of entering a fictional space separate from the 'real world.' The details of actual history serve to ground the story, help support the suspension of disbelief, not educate the reader about life in castles.
So how can such cavalier appropriation provide any actual insight into the past?
Fantasy does have a value to serious inquiry into historical periods. Firstly, when a writer such as R. Scott Bakker weaves elements of actual history (in The Prince of Nothing's case the First Crusade of 1096-1099) he or she is encouraging curiosity in that time period. Even a very casual reader will recognize the descriptions of the Holy War of the Three Seas as paralleling the Crusades, with the Thousand Temples' new and fiery Shriah Maithanet standing in for Pope Urban II, the Fanim states instead of the Seljuq Muslim Empire and a beleaguered and crafty emperor Xerius for the Byzantine emperor Alexios I Komnenos. These parallels are obvious but they're not exact. Bakker crafts the culture, language, and religion of the factions in his novels with elaborate care and ingenuity. The effect is one of suggestion. While the novel may certainly be appreciated on its own merits, a reader often finds himself distracted with a simple curiosity: what was this period really like?
So, on a very basic level, fantasy does lead readers with a very cursory knowledge of a certain historical period into greater knowledge, deeper insight. If the work of fantasy is well done, then it doesn't suffer much in the comparison, only benefits from association. If the fantasy is mediocre, then this hypothetical reader will still be enriched by the discovery of actual history.
But this is a very thin reason for reading fantasy, and poor apology for its short-comings. By this line of thought, fantasy becomes useful only in its relation to some other historical period, the choices an author makes enslaved to often deadening questions of accuracy and verisimilitude. What sorts of weapons did the Crusaders use? What kind of food did they eat and did the writer get it 'right' in volume X?
What I find compelling is something's significance or lasting importance. From that standpoint, historical fantasy often loses out if merely judged on its relationship with some actual historical period. However, I do think historical fantasy has a lot to say about the time period in which is produced. Bakker's Holy War fantasy might not have all that much to offer for scholarship of the High Middle Ages, but it has plenty of value for commenters on today's culture. What does it say about our time period that a description of a Crusade embraces so many separate view points, focusing on the each characters' complicated political machinations? What sort of critique does this story offer a modern world riven with ethnic and religious conflicts, where the struggles of great powers are simultaneously cloaked in secrecy and routinely revealed in Wikileaks?
To take an extreme example, the movie Avatar pounds the viewer over the head with parallels with the colonization of the American West and Imperialism in general. I don't think anyone would want to use the movie to learn about First Nations but it might still be interesting for some future historian as an example of the dominant contemporary culture coming to grips with the legacy of that conquest.
The use of science fiction and fantasy tropes to cloak painful truths in appealing allegory has a long tradition, one that might say more about the period the work comes from than the one it borrows from.