I don't know that I've ever seen her come up much in a game, but I'd interpret them both as "anchor points" essentially. If the board gets nuked, anything connected to them stays, and if things connect them both they stay as well. Things would only be discarded if they aren't connected to either.
The real issue with her is probably that Shai Ni still is a Pony card, so there might be some weird interaction with some card that affects Pony cards and her. Just Starlight her and get her off the board as soon as possible I suppose if she's an issue.
EDIT: Actually, the more that I think about it, you're probably correct with your interpretation. It's really up to the players, since "counts as Fanfic Author Twilight" could mean she's considered a Start card as well, though I interpreted the "with all her keywords and powers..." part as an explanation of what "counts as Fanfic Author Twilight" means (which doesn't mention her being a Start card). You may want to contact Horrible People and see if they might be able to clarify further.