I always interpreted it as Jake ordering the erasure of too much memory. His passive powers seem to operate by burying a person's thoughts until they're just subconscious or rewriting the memory, but his active command seem to outright force someone's brain to delete it. Jess didn't react that way when ordered to forget something but it would likely only be getting rid of minutes for her. But Mia would have every stray moment where she thought about Ella's existence and Jake's powers purged from conscious and subconscious memory across days.
Considering the brain technically permanently reshapes itself every time it stores something in memory, with long term memory requiring bigger and more structurally significant changes, I can only imagine the kind of strain having a big chunk of your synaptic connections forced to break up and warp beyond all capacity by a supernatural foreign power would bring onto someone. It's not a slight twist or shuffle like misremembering something, small to medium subtle corruptions of old memories happen without you noticing everyday. Maybe you were fatter back then, maybe that shirt's the wrong shade of green, and in your head a shout or a whisper is equivalently loud. But to outright purge everything, wipe the slate clean and force the pieces to never be allowed to be whole again? I'd imagine it'd just be too much happening too fast.
My idea about what happened is something like this:
1) When someone actively resists Jake's commands, Jake expends power to enforce it. This is shown in the prison segment where he does a power contest with MC.
2) Jake has an easier time applying his commands when the target is unsuspecting. This is why Ella tells him to be very careful with his commands during the HERO infiltration and how he even managed to influence Alexis.
3) Jake's perceptions and emotions affect the effectiveness of his powers. At first he had a lot of trouble with Jared, till Ella beat the shit out of him. It's possible that the only reason he managed to control Jared was that he was more afraid of what Ella would do to him if he failed.
4) Mia, beyond all reason, manages to resist his command for a time. She is a human and not even a savvy/seasoned one. So it stands to reason that Jake's feelings messed with his power and Mia resisting made it even harder.
This makes me think that Jake had to expend way more power than he normally used to break through his own feelings that held him back, and it's what caused his evolution. He was in a power contest with Mia, a human, and he evolved while the "link" between them was still active. The power of the command jumped manyfold the moment his power increased and broke her mind.
There's also indication that Jake monsterfied partially. We have seen superhumans with weird characteristics like Klaus, but his were even more pronounced, with monsterteeth and the peculiar eyes. Additionally, his evolution seemed particularly painful, remniscient of Deryl's monsterfication.
The game suggests that monsterfication makes the individual significantly stronger, so even a partial one could raise his powers very sharply, similar to how MC got a 15 power boost in deadend1.
