Anthony, the SB3 program makes no attempt to correct for installation geometry. That is the job of the toolpathing software.
There are commercial toolpathing programs that can do that kind of computation automatically. I found the cost to be pretty high, so I designed my own parametric toolpathing program in C#. It can do that kind of operation and (of course) is correct for my bots configuration (only).
If you know anything about programming (it seems you do) write a toolpath generator that does what you are looking for. You will probably find that route will be most satisfying. (And also break the most bits!) Check the output carefully.. the voice of experience here.
Good luck, looks like you are on to some interesting stuff.
D
"The best thing about building something new is either you succeed or learn something. Its a win-win situation."
--Greg Westbrook