While the pregens are based on the Undercover Agents and Unwitting Investigators, the information presented in the base zine is for the GM. So when you’re playing Triangle Agency, your players will have to contend with those Unwitting Investigators, some of which may be connected to their player characters in some manner (regardless of whether or not they’re using a pregen). So the relationship hooks listed for those characters assumes you’re using them as NPCs while playing TA.