It is possible that different software handles different file formats differently and the results are not exactly the same.
However if this were the case it would be the programming of the software used to produce or read the file formats that is different, and not the format, and the results could be different in each specific case regarding which is better or preferred.
Format does not assure sound quality. That is evident with records, tapes, CDs, you name it. Different versions of the same material in the same format sound different because of the way the recording is produced despite being all of the same format.
In the case of flac versus .wav, I would expect if everything is working well, and the resolution of the files are the same, there should be no inherent difference in sound quality resulting from format alone.
However if this were the case it would be the programming of the software used to produce or read the file formats that is different, and not the format, and the results could be different in each specific case regarding which is better or preferred.
Format does not assure sound quality. That is evident with records, tapes, CDs, you name it. Different versions of the same material in the same format sound different because of the way the recording is produced despite being all of the same format.
In the case of flac versus .wav, I would expect if everything is working well, and the resolution of the files are the same, there should be no inherent difference in sound quality resulting from format alone.