I'm not sure what you mean by "individual microphone capsules". Are we really talking about the Main and Secondary Microphones in MIR, or the so-called MIR Icon that's used to represent a signal source on a stage ...? :-/
MIR Pro's output will always depend on the chosen Output Format. This can be set up in the Output Format Editor window. It is the combined result of the (virtual) Main and Secondary Microphone capsules and the Matrix settings used to distribute them amongst the actual "physical" outputs. So as soon as you would assign _one_ capsule to _one_ output channel in the Matrix, you could make seperate tracks for them.
If you need a 5.1 (or 7.1 or Quadro) output format from MIR Pro, simply instantiate your first MIR Pro plug-in in that format. In some hosts like Cubase and Nuendo the respective track would have to be in that format already, in other hosts like ProTools and Logic you are free to change the number of the plug-in's output channel by selecting the desired plug-in format. I can't tell you which approach Reaper adheres to, sorry to say so.
In any case - the "force output channels" preference isn't a tool for daily work, but a purely technical option to circumvent restrictions imposed by certain DAWs.
HTH,
/Dietz - Vienna Symphonic Library