There's no "decoding blackbox" in MIR 3D at all, just state-of-the-art Ambisonics decoding, wrapped up in good (I hope!) audio engineering. Just open the Output Format Editor, and you'll see that every parameter is accessible.
However, as soon as you listen to a 3D setup on stereo headphones without manual downmix parameters or a binauralizer you will indeed just hear something arbitrary. Hard to say what happens in your DAW when you do that: Maybe you're just listening to the left and right channels, maybe to a uncontrolled mixture of all channels, maybe something created by an automatic mixdown process - no idea. If you like the sound, just use it, but I can't tell from the distance what it is.
Of course Dear VR Monitor narrows this uncontrolled image with its hard left/right panning. That's actually one of the strongest points for this kind of processing: You get rid of that silly "In-head-localization", even when your source is just stereo. ... the fact that we can hear sources from the back and above to a certain extent by means of binauralization comes as added benefit, actually. :-)
No idea where the echos you seem to experience come from. Maybe time to get in contact with the nice people of Dear VR directly ...?
Kind regards,
/Dietz - Vienna Symphonic Library