I can’t answer you this in detail, that would require detailed analysis of the audio file and fingerprint generation at each step and I don’t know the algorithm good enough to do this.
But you basically gave the answers yourself in DJ promo releases - #112 by thwaller . Lossy audio codecs are lossy, the decoded audio is different from the source. You even said you could hear a difference (I can’t, but that doesn’t say much ).
That also means the fingerprints, while reasonable stable, differ so slightly. The important characteristic of the Chromaprint fingerprints is that they are comparable, so you can tell how similar two fingerprints are.
And that’s where the AcoustID server comes into play, it compares fingerprints and groups them together into tracks aka AcoustIDs. Actually there are even two levels of this similarity comparison: Very similar fingerprints are indeed just treated the same, so when you submit them they just increase the submission count of the existing fingerprint. And then there is the grouping of similar fingerprints above a certain threshold into AcoustIDs.
You can actually see this now at https://acoustid.org/track/f7f3ee20-7c6b-462a-9188-73a063605970:
Originally there were only two fingerprints, 89447221 and 89447222. These were for the two files from your ZIP. Now I generated different encodings from the WAVE file and submitted the fingerprints for 9 different of them. Actually each fingerprint for 288 kbps and below is a tiny bit different. But the import caused only two new fingerprints in the AcoustID database, 89474492 (which grouped 8 of the submitted fingerprints, meaning they were really really close to one another) and 89474493.
Also interesting might be that all the encodings for 296 kbps and higher up to 320 kbps produced the bit by bit identical fingerprint. So encoding quality surely has some impact. But in this example it is clear that there is some minor but notable difference to the WAVE, but all the files encoded at 296 and higher give consistent decoding results. This might be something very specific to this audio in regards to the encoding algorithm.
Also it is important to stress that you cannot generalize this. You can’t say “Fingerprints for MP3 encoded with 296 kbps will be more different to the source than fingerprints for 288 kbps”. As I said in the other thread the MP3 in my collection, of which most are encoded with 320 kbps, very consistently give the same AcoustID as the FLAC file they are derived from.
Overall while this is a very interesting case this all is neither unexpected nor surprising. As I said in the other thread this is all about comparison of slightly different data for similarity. And inevitably there will be these cases where things are just beyond the used threshold.