I've been playing MP3 for the first time lately and I'm excited for this next entry! I'm glad to see they have seemingly introduced a new nemesis, as dark Samus was getting a little old IMO
If you look closely, you can actually map the letters mp3 to the first letter in each of the words from the phrase metroid prime 3. This is some advanced cryptography so let me know if that's hard to understand.
It definitely comes off as them demanding someone spell it out instead of using an acronym, but you're right I should give them the benefit of the doubt.