I have ATC SCM19's, Musical Fidelity M6si, Lumin D1 streamer and a Denafrips Ares II dac.
I use four subs connected to the MF via MiniDSP 2x4.
I am still tweaking the setup because the speakers a relatively new to me and I have reconfigured my listening space. Despite this the low end sounds very good to me, but I certainly appreciate your frustration. There is such a range of bass content and quality in music that it's hard to tell if an imbalance is your system or the sound mix. Either way I don't think anything but the lowest tones should be unrecognizable or boomy. If they are, it might be a result of the placement of the subs, the room itself or a combination of both.
Also, I am curious about what you feel is a "very challenging room"?