Creating Scenarios for Mansions of Madness
Ok, so I'm answering my own question, at least in part.

First of all, I think the internets were greatly deceived when they spread the idea that each of the five scenarios (there are indeed 5) had only three variants. Some of the scenarios had what looked by my calculations to be upwards of 40 permutations. 

Second, the Keeper's role is much more dynamic than I had previously realized. It strikes me that the Keeper's game is similar to the Demons' game in claustrophobia, a truly wonderful asymmetrical 2-player game. Like the Demons, the Keeper accrues Threat over time, which he must pay for all his actions. It seems to me that the vagaries of Keeper play will keep even an identical scenario from playing out the same way twice. 

Finally, I think that the answer to my hackability question is a resounding no. The thing that has me so excited about MoM is that it provides narrative out-of-the-box. The game does a lot more storytelling than most. That very quality seems to make it hard to vary beyond the included scenarios. Each card is tied tightly to a choice or combination of choices and the stories will fall apart if not constructed properly.

This is my opinion as of having read all the books, but having played zero games. I will update this answer if that opinion changes.