I’m not really sure what’s going on behind the scenes with Core Decoder on vs off in Roon, but I think you are on to something
This is likely similar to what is going on with some DACs featuring MQA decoding. I have not done extensive testing, but I suspect there are cases where it could be messing with the data when it shouldn't.
On a whim I turned it off today, playing Hires via Qobuz sounds better to my ears when core decoder is off rather than on. Better dynamics, perceived loudness, bass impact. Could be placebo, but it’s almost like there is some additional processing happening in Roon (even on non MQA content) when Core decoder is toggled on causing compression / loss of fidelity.
You could try playing Qobuz with just HQPlayer Client for comparison. In that case you know there's no MQA or similar sitting on the path.
From mathematical perspective, both Roon (with all DSP disabled), and HQPlayer playing the same content from Qobuz should have same result.