The problem arises when these signals are combined. As you can see in the next chart, there is a big bass cancellation caused by a mismatch in phase, when the LFE/Subwoofer and the left channel components combine.
I ran a simpler test and cannot reproduce this, there isn't enough detail in how you have MC configured to know what is different though but I think this is a straightforward test of whether jriver DSP is doing what it says it is
* create measurement sweep in rew, save as file
* set output format to 5.1, no JRSS
* turn off all processing
* add room correction, set L and R channels to 100 Hz / Move Bass to Subwoofer / both dropdowns at 24dB/Octave (i.e. 4th order butterworth filters)
* set output to disk writer
* play measurement sweep
* import sweep recording into REW (channels 1,2,4)
* verify that L and SW are filtered as expected
* add PEQ block after room correction
* add mix "Add Sub to Right"
* play sweep
* import R into REW
* verify that resulting measurement has expected +3dB hump at XO frequency (usual for BW filters)
IMV this is a "pure" test of MC room correction as literally no other component is involved. It works as expected for me except for one thing, the SW channel outputs 4dB too low. This must be a jriver DSP bug but no clue where that comes from.
If you see large cancellation (timing error) then there must be some delay being applied somewhere in your chain that would cause this.
Note that I don't disagree with your core point which is that jriver needs to improve how it handles low/high pass filters & also how bass management works, I think it's quite hard to recommend using it as is. Unfortunately DSP has seen little attention for some years so one might not be optimistic about that changing.