Not directly related to the Weiss DAC, but when I did a comparison of Qobuz files, my own ALAC files, Qobuz directly or Qobuz via Roon on my T+A DAC, at no point did I notice any different audio quality. As far as I could tell, they came out exactly the same (and in Roon, the signal path always had the “purple” light). Of course, I have within Roon the option to adjust the sound or use volume leveling etc., all these options are turned off in my setup.
The Weiss is a high-end DAC, which means: there shouldn’t be any difference in audio quality, regardless of how the files are delivered, and regardless of where the PCM gets decoded. In theory, there should be no difference, period. In the end, it is the PCM that gets converted to analog in the DAC, and the PCM should be literally the exact same, regardless of whether Roon decodes the FLAC and sends the PCM to the Weiss, or the FLAC gets sent directly to the Weiss, because in the end, it is always the PCM that gets “played”.
So since you hear a clear audio difference, and since apparently “Weiss had received several similar reports regarding Qobuz Connect versus Qobuz via Roon” and are actively investigating the matter, this seems really a very interesting and even unusual case.