When committing two Action tokens to gain the benefit of an Aptitude for defense as a Desperate Reaction, do those tokens have to come from the pool, or can they be transferred from a committed stack? I guess the latter case would count as Reallocation and cost Fatigue, making it a worse deal than the other option for Desperate Reaction of spending a token, but if the player is all in, it might be his only option.

Correct! They may come from the pool, but if they come from another committed action, they count as a reallocation.