Why do Wav and Flac Files Sound Different?

Do you all understand that the metadata and music data are not in the same places in the file or is that ... not relevant to this discussion?

The metadata, if read at all, is not interwoven with the music stream.  It's a completely separate part of the file, and from a performance issue, adding/removing files from one folder to another in a hard drive is no different than adding or removing another software program or game to your hard drive.  If these make a difference to your sound quality there's a very big error happening somewhere.

Well, here is something else which may have triggered my initial puzzlement. When I used to download .flac files from ALLFlac.com I wasn't removing the metadata folder when uploading them to JRiver. However, after converting them to .wav in JRiver the metadata would be stripped out. The new CD that had been burned from the .wav files had no way to be fetched as separate tracks on my transport. What came up on the transport's screen would be the number "1" and it would be unresponsive to the track selection button on my remote - all that was visible during the entirety of playing the CD would be that "1" staring me in the face. The tracks would be in the right sequence and the silent gaps between tracks would still be there, but otherwise the only option was to listen to the entire CD in one fell swoop.

Perhaps this could be described as a "bug."

I can believe that.  I've owned both JRiver and Media Monkey.  Honestly not a huge fan of either's UI, even less Qobuz, but I do think Media Monkey has a better overall handling of metadata. Do I think it affects the sound quality?  Absolutely not.