...But here, he knew what it does because he was told about the pill's side-effect but decided to use it to fulfill his lust for his mother. I don't know, maybe I just find the mental manipulation with emotions worse than a manipulation with a spell.
As I said I'm not too far in the game so I don't know the contents of the different paths, this is just my first opinion on the MC and I seem to be wrong on him.
No, he don't uses the side effect on Megan/Mom, she acts on her free will, she only wants to help her son, that this escaletes into more is kinda caused by his and her hornyness. Later on (Chapter 4.2) it happens by accident (on Corruption Path). But at that time they already had gone the whole way, and she was reluctant because of her guilt for what happened a few days earlier.
He uses it on Doc Wood (but that was by accident too), Jack's Mom Faith was because Jack plead him to do so.
Pill or Spell is kinda different. You CAN decide to use the Spell, or let it be, but you cannot control/predict the emotions of other People, everything happens by coincidence.