I'm not surprised one bit. Fowley looked exactly like he was. And even back then it was clear to me that The Runaways were puppets at his mercy, molesting included. But I believe that even as a 16 year old you could sense that the man was evil and scum, Frau Fuchs realized that probably earlier than others, but the girls went for a Faustian pact (for a while at least). The Runaways film was surprisingly light on that shady part, but it seems that band-internally it was and remained a non-subject, never mind how unsurprising it all is. I don't doubt Frau Fuchs' story either. That JJ refuses to confirm it is again no surprise - she was probably just more hellbent than her bandmate in selling her soul and took it as part of the deal, especially if it is done to someone else and not her. JJ wanted fame at any - even the highest - price and she got it from Fowley. Stalking Suzi Quatro (and looking like her) only gets you that far.
There are people you just look at and your sensory warning system goes off - Kim Fowley was an arch example. Bill Cosby was way better at hiding it.
BTW: I wouldn't be surprised if there were male bands with similar experiences with gay managers/svengalis too. And that it remains hushed up.