As I understand it, WMA files must be read then decompressed then processed by BIAB. Flac files must be read then decoded then processed. WAV files are just read and processed. That explains why I think the priority you were given is not correct.
As I understand FLAC, to create a FLAC file the source is compressed using psychoacoustic methods, then decompreseed and a difference correction track is produced from the differences, which correction will be applied when the FLAC is expanded. So on pure processing time from file to usable data, WAV would be quickest, then probably WMA, then FLAC.
However that does not take into account the time taken to read the data from the media. With spinning-rust hard drives, that time is likely significant. I suspect with SSDs, rather less so, or possibly not at all.