Firstly, I recommend measuring this to verify the behaviour is exactly as you expect -
https://wiki.jriver.com/index.php/Verifying_DSP_Studiobut lost on the 2 channels in a 5.1 container (and is that the right setting? Why not 5.1?).
this is covered
https://wiki.jriver.com/index.php/Output_Format#Understanding_the_Channel_Options it's due to the way MC conflates the mix target with the number of physical output channels. 2 channels in a 5.1 container means "create a 6 channel output device, mix content to stereo" whereas 5.1 means "create a 6 channel output device, mix content to 5.1"
In your case, you have the correct option.
What is JRSS doing in this particular scenario?
jrss mixing means downmix 5.1 to stereo and pass stereo through as is except that you have...
What is being low passed at 45 Hz to my 3 way stereo system? Or does any or all of it even apply in my 5.1 to stereo scenario?
See
https://wiki.jriver.com/index.php/Output_Format#SubwooferAs far as I know, this is basically a double bass option. It will copy some portion of the main channels to create a .1 channel.
In your particular case, I have no idea what it will do. Some things I can imagine it doing....
* ignore the setting completely
* fold that content back into stereo mix (i.e. adding that option creates a 2.1 feed from stereo but the mix target is stereo so move that bass back into the mains)
* throw away that content (i.e. discarding LFE on downmix)
or it might do something completely broken like see 6 channel output and leave it on channel 4 (obviously a terrible thing in your case).
This is definitely a case where you should measure to see what it does.
Having said that, in your case, I think you should simply turn it off.