Hm, and I'm only a Delphi/pascal guy... and never will the two meet.
What if Bongo would read, on demand, a "declarative" external data format for the joints & other definitions? Of course a "live API" would rock, but if Bongo could configure a model on demand from imported constraint declarations, it would be a significant first step in enabling the outer non-bongo space to communicate with Bongo.
Perhaps it would even suffice as a solution in most cases. Different ways to trigger Bongo to reconfigure according to such a descriptive file would be an API call ("reconfig") or even a file modification in a dedicated file or subfolder would do (with a Bongo option set to "listener" state).
Somehow Bongo already stores the "declarative" information it currently makes use of, just add a step in which that info is inserted into the model by import, and off you go.
Which gives me the idea to ask if that stored info in the model is accessible (read/write) through the "regular" Rhino API, and if Bongo could be "paused" while modifying this info?