As stated above, Qobuz gets its files directly from the record companies that control the content. Qobuz never gets within a country mile of a master tape - they just take whatever digital files are given to them. There is good evidence that some of their files are actually MP3 quality that has been put in FLAC format (you can test the bit rate in Audirvana and other computer music programs). This is not Qobuz' fault. They came that way from the record company.
I have never seen information about how the record companies come up with the digital files they submit to Qobuz. As far as I know, this part of the process is a black box. I would think that they would generally use the WAV file from the latest version of each title but who knows?
FWIW, I have compared several CDs to their Qobuz counterparts, being careful to use the same version, and they have all sounded identical to me.