RTF is a global modification that replaces all towns in the game.

In other words, does this imply that dwarves, chimera mages, and orcs should be dark chaos factions, which is why the schools were mixed? But now, as a result of the mixing, they will completely lose their clear focus on darkness/chaos, gaining the ability to use spells of a completely different kind.

Not exactly. We simply decided to show that these factions are "bad" in this way. Giving orcs/dark dwarves light or summoning spells would be strange, wouldn't it?
Besides, each of the elements does not represent good or evil (or partially (summoning demons/archdevils)) and can be distributed more freely.