I see absolutely no
indication that what is there now (talking about the cape-ell connection) was ever changed. No nail holes, and what signs of earlier damage is there to indicate that the entire roof was replaced? That would be a far reaching scenario I think.
I think Jeremy has pretty overwhelming evidence that the house is pretty much exactly how it has always been. I myself find it to be a fascinating house and should be celebrated as such..
Anyway, I think if Jeremy gets to his town hall records room and starts with some research of deeds that he will start to solve the mystery in more concrete ways.
Jeremy, there may be another hole in that stack under the woodwork maybe??
Here is an interesting illustration from Big House, Little House Backhouse Barn.