It might be worth posting a recording. It's very hard to describe sounds with words
I think the volume level on the speakers doesn't mean much in isolation without knowing what the input signal is. For example, two different sound cards can produce very different SPL even though both were at max volume:
https://www.audiosciencereview.com/...s-powered-active-subwoofer.68573/post-2609438 The only way to compare volume is by measuring the SPL. You could try some free meter apps like Decibel X and NIOSH SLM to get a rough idea.
40Hz is pretty low for the MR5s. They are very attenuated at that frequency so if you're pushing loud at that frequency, you might just be pushing too hard. Do you hear any issues with normal tracks or only the Lo groove one? If only the latter, it's potentially just not something to worry about. That track I would suggest is more aimed at sub woofers that can push down to 30Hz or 20Hz at volume. Listening to it on the MR5s without a subwoofer, I suggest you should expect it to sound "great" but be missing sub bass. Whereas if you're expecting to hear the sub bass and have the volume up enough to hear it, you're probably pushing them too hard.
I would also suggest physically swapping the speakers when you reverse the channels in the edifier app. That will help identify whether it's a placement issue or inherent in the passive speaker. If it's placement, then the issue will now appear to be with the active speaker.
I would also try moving the speakers off the dresser onto something else like chairs, preferably something open all around. This would rule out interaction with the dresser.