I really wish you always got the option to pick a hero from your own faction (as one of the three) when acquiring a free hero. It should be the case that one of the three is always a hero from the player's faction, while the other two are chosen randomly from the current game mechanics. If a player rejects the selection of that faction hero then it could become available in the pool (or market) for anyone. That would be more thematically interesting, and also strategic because the faction heroes have unique skills that compliment the faction and you can play towards them, instead of not knowing what you'll get.

I think they intentionally do that from a lore perspective, because these heroes are essentially free agents with arguably more allegiance to the Academy than a major faction. It's more evident in their back stories. From a gameplay perspective though, I just rather have more potential access to my faction's heroes than the game provides.

There is a mod that I recall, but I think it dumps all the heroes of your faction on you at turn 1.