I'm not having any of the issues you describe.
Unless you are playing at/above reference level (...and even then...), it is highly unlikely that your Buckeye is root cause.
My uneducated guess is that you may be experiencing either or both of these issues:
(1) You may be driving your R3Ms with music that has a larger percentage of information below 80Hz coupled with a higher volume setting on your Denon.
(2) Your source may have some measure of distortion contained within the music that is being amplified and then fed to your R3Ms.
For issue (1) you should set a proper crossover between your R3Ms and your Sub, start at 78-80Hz and then work your way up until you resolve the issue.
I've changed a number of pieces of gear in that system:
Bluesound Node 2i - miniDSP SHD - Buckeye NC502MP - KEF R3 (non-Meta) + Emotiva SE12 Sub
I have the speakers about 1.5 ft from the back wall, about 10 ft apart, the port plugs IN, and the R3 crossover set at 100Hz with 24dB/octave slope on the miniDSP SHD.
As I mentioned above, zero bass distortion issues. In fact, it sounds amazing.