Fascinating article, Marilyn. Thanks for posting it.
As for your question, I think there's no definite answer. Imho (and I could be wrong), short stories (say, below 100kb) tend to follow the latter structure, because there is less conflict introduced and they're mostly romance (in the Lois and Clark fandom, that is), whereas longer stories, and even more so epics, are closer to the Aristotle structure. Very often, they follow a traditional narrative structure, with an initial situation, a conflict that throws said-situation off balance, additional conflicts that are usually consequences of the initial conflict, a climax, an epiphany and a denouement. At least that's my own perception of how many long fanfics are written, though I doubt authors do it consciously.
Kaethel