One of the significant differences between most historical Total Wars and the Warhammer games is that the factions aren't comparable with nations. In Total War: Warhammer 40,000, the Space Marines and Astra Militarum, for instance, are effectively two branches of the same military...
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Total War: Warhammer 40,000's Space Marines will have to keep the Imperium happy and avoid looking too heretical
Source: PC Gamer (opens in a new tab)