About the only thing I can say about the Farm Ferry project is to contact either the designer or the engineer of the project. They should be able to give you the answers to why such a joint was used.
And about the Rindge Meetinghouse, you could try to contact the guys who wrote the articles and see if they can shed some light on the reasons why they did what they did, way back then.
Good topic, and good luck with your research.
Jim Rogers