Just to verify something. If I was to switch from stereo to multi-channel, any FX on the output bus 1-2 will only apply to whatever is going to end up going through bus 1-2. This has not always been the case, has it? I swear I've not run into this in the 2.X versions. It sounds obvious and matches reality, but then getting a multi-channel output bounce to match a stereo bounce becomes a nightmare.
I tackled the issue like this on a small bit I was doing. The SD3 preset had lots of outbus FX going on.
#1: Saved each bus 1-2 effect as a user preset.
#2: Created a new group bus.
#3: Instantiated a copy of each plug on the new bus, setting each one to it's preset I had just saved.
#4: Ran post-fader sends from the rest of the buses to this new bus.
#5: Selected multi-channel and assigned the buses to the out-buses accordingly.
#6: Muted the plugins that were left in bus 1-2 (used with the stereo output)
#7: I tracked the outputs, including the new effects bus, in my DAW to respective channels.
I compared the output from a Stereo "bounce" I had done and the new multi-channel. It was very close. I ended up lowering the volume of the new FX bus I created on the multi-channel outputs by Something like 4-6db. After the bounce, an additional 1.2db narrowed what was left of the gap. A large part of this SD3 kit preset came from the master out-bus FX as seen in the stereo mode.
I hope that I have missed some sort of obvious functionality somewhere or that my workaround can help someone.