What I've noticed in my case is that yes, I now do think I could feel like a good person even if I do bad things to others. However, I now genuinely don't want to hurt other people.

Yep. Motivation is not symmetric.

What used to boggle my mind about this, is how it could be that our brains are built in such a way as to seemingly automatically believe that motivation is symmetric, even though it isn't.

My working hypothesis is that the part of our brain that predicts other minds -- i.e. our built-in Theory Of Mind -- uses a symmetric model for simplicity's sake (i.e., it's easier to evolve, and "good enough" for most purposes), and that we use this model to try to predict our own future behavior when anticipating self-modification.