If you use one of several programs to compare those decoded WAV files (Foobar 2000 has a free plug-in which does this; I think audiodiff maker is also still freeware) you will find that they are identical, both audibly and as data files. Before you argue that the sound is more than the bits, check out those apps. They take into account aspects of the data important to music, such as jitter and phase, they aren’t bit comparisons. If you are comfortable using an audio editor such as wavelab, samplitude, soundforge, etc, you can devise your own comparison algorithms.
As I said, though, on the fly convertors may differ. Have you asked this question at audiophilestyle.com?