They've deliberately picked an era where they had free rein with the lore and story without treading on the toes of existing canon, yes - I think that's a shrewd move, allowing them to explore an interesting unexplored time and giving them some breathing room to do what they want and what is good for gameplay.
and yes, Nosgoth has some fantastic gameplay, interesting mechanics and is a little unusual and different from your regular multiplayer experience - that all helps to make it a worthwhile game to make, where previous cancelled projects perhaps weren't and that will help get the series fans who'll help justify further entries.
As for the humans, you swap sides midway so neither gameplay team has an advantage and the humans really are an effective menace to the vampires: that's why they're getting their own fans. All we really know about what happened eventually is that the humans were reduced to a single settlement while the vampires were reduced to devolved beasts, with the sanctuary of the clans "reduced to ruin" - so who actually won?... and vampires don't use or need guns