“Only too well” is used to emphasise that you wish what you know wasn’t true. 'he remembered their power only too well' means that he had some kind of unpleasant experience because of their power. Other examples: 'I know only too well what it's like to lose someone to smoking' ‘I know only too well how unpleasant it is to have one’s leg amputated without anaesthesia’

Okay, I am not a native speaker, so I will only post my views as a comment. But: In my opinion they mean almost the same thing. Only the 'only too well' has a slight nuance in it that he was confronted with their power before. So he knows their powers really well, but not from hear-say. Probably from being confronted with these powers before. Also the difference between knew/remembered emphasizes this. Apart from that it is just a different way to say it, let it sound more poetic, stylish, narrative. But, may any teacher or native speaker correct me, if I am mistaken!