Ah, so you dont need to have the both outputs active at the same time. That would work in similar way MPAR - just change the registry settings before starting the playback with similar way as you are now changing.
I do need to have both outputs active at the same time. If I'm using "Stereo to two outputs" it's sending the Stereo signal to the L&R output and the Centre&Subwoofer output at the same time. If I'm using "5.1 mixed down to three channels" it's also using two outputs, the L&R output for everything but the Centre channel content, and the Centre&Subwoofer output for the Centre channel content.
Whilst I could still use ffdshow's mixer profiles to mixdown as I am now before sending it to MPAR, the way ARC works is it loads the ffdshow registry settings for one or the other profile and switches renderer to trigger a rebuild of the graph. Currently it's set to switch between Default Directsound and Directsound: Realtek Speakers, which isn't really a switch at all as they're both the same thing, but the different name is enough to trick ARC/Windows into rebuilding. Obviously I can't do this with MPAR as there's only one instance of it, so I'd have no way of switching the ffdshow profiles.
MPAR will output stereo as stereo if no force mixing option is selected.
Oops, should've been able to work that out for myself from the first post! So I could use ffdshow to mix "Stereo to two outputs" and "5.1 mixed down to three channels" and feed that to MPAR with ForceChannelMixing disabled and it would just output whatever it receives (both profiles actually use four channels/two outputs so I suppose I'd set SpeakerConfig 51). I'd still need a way to switch ffdshow profiles and trigger a graph rebuild (using a remote button) though.