Possibly because it feels like the resource most fitting for the purpose. At least to me, souls thematically makes more sense than maps, glory, traitstones, trophies or gold. What I definitely do agree with, it can't be souls alone, there has to be some other limiting factor to prevent players burning though stockpiles.
Personally, I'd prefer some daily log in related restriction, something like crafting a single common requiring one daily token, crafting a single mythic requiring, say, 60 daily tokens. Add a reasonable soul cost (because troops = souls) and maybe a few gems (because picking the troop you want = premium).
Should work out okay for all players. New players could craft a cheap common/rare/ultra-rare to complete early teams that are missing a synergy troop, about one every few days. Long-time players would save their daily tokens for missing legendary/mythic troops, about one every other month. No P2W, buying souls/gems won't get you every Mythic in the game on day 1, you still have to collect enough daily tokens first. However, buying souls/gems may allow you to craft the troop you want right when you have collected enough daily tokens, which I'd consider a good thing for games not run on charity.