RS4, I actually decided to not swap after I made the post.
Why do you say to stick to the f box out of curiosity?
Well you have an RS4 so why not run code written for the RS4? The M-box has been dialed in for S4 hardware so it does not have support for things that are in the RS4 like the air box flap opening valve. It also does not have a 16 bit load axis. The RS4 has different throttle body, different intake manifold and so on.