Same is true for Jade Cocoon and Kileak, Matsumae often re-records and re-mixes his music for soundtrack releases. Actually, pretty much all current-gen albums are similar to this since the music in-game is often interactive and thus built in a different way. The album releases are "arranged" as linear musical pieces to fit the format. It's just something that can't be escaped with game music that is often interactive and/or relies on the hardware/software for in-game playback. Another example is soundtracks for gameboy/NES games that might not use the original hardware but an emulation instead, should we classify them differently too? I don't think so
I still think it's a minor issue but it's interesting to bring up, I personally don't think we need to take any special action.