You're reading of the WAADC is missing out a crucial part - it says education only activity *organized* by a member federations, or member federations affiliated club, or activity involving athletes of member affiliated federations/clubs.
The general read on this is she can't train not just with anyone from BTC, but not even an 85 year old masters runner so long as they have a USATF membership or any other national federation membership. Cant use facilities supported by funds from USATF or affiliated club.
There's a couple of gaps in the rules here for Houlihan though. It does not say she can't go to a track at a time that it's accessible to the public and use it as a member of the public would. So she's fine there.
She could still feasibly be coached by Schumacher legally in my opinion, she would just have to pay him for private coaching services. I used to be coached by a div1 track coach though wasn't on his team; I paid him to coach me privately on the side and so a lot of my workouts and how my training was structured looked the same as what that NCAA team did but 1) I clearly wasn't on the team and 2) as I was paying him, I wasn't just freeloading off of the team. To be clear I wasn't serving a ban, but I don't see how what I was doing wouldn't be allowed under the code so if Houlihan did something similar I don't see how that wouldn't be allowed either. It's kind of a loophole, but these rules are pretty vague. The key word "activity" isn't even properly defined.
The big piece where I am curious how she is managing is pacers. Presumably she isn't running these times completely solo and has at least one pacer, probably male, helping her. Per the rules the pacer wouldn't able to be a registered member of USATF (or other federation), so she has to either have found someone fast enough to pace her that also isn't doing any sanctioned races otherwise or she is breaking the rules on that front.