Any current Japanese videogame development company that creates games with the intention of releasing them to markets outside of Asia would in most cases be conscious that there's a strong possibility that things will be tweaked for the international versions of their games, including the soundtrack.
In addition, unless a videogame is developed by a handful of people in a basement, even the strongest of artistic intentions from the creative force behind a game will become watered down and compromised along the way by factors of practicality and commerciality. For all you know, a few new songs for the Western release of a game could be one of the least significant compromises of the game creators' original artistic vision, if they had an artistic vision to begin with.
For me personally it can go either way, depending on each individual case. Using two examples that people have mentioned already, on the whole I preferred the original Japanese/PAL Sonic CD soundtrack to the American one. One of the most crucial elements to the Sonic series at the time was the style and the music. The year that Sonic 2 was released was the year that the composer of that game's band, Dreams Come True, released what became up until that point the highest selling Japanese album of all time (which incidentally featured a fully fleshed out vocal version of Sonic 2's theme song), and while neither of Sonic CD's soundtracks were as good as Sonic 1 or 2's, Sega in Japan would have been very conscious of the importance of music in Sonic and people's expectations of that, and the original Japanese/PAL soundtrack delivered. While the American one wasn't bad, it was a bit flatter and less lively and colourful, and I didn't think it was an appropriate soundtrack for a Sonic game at the time.
On the other hand I thought that the original Japanese theme song to FFXIII was just another tragically boring, sappy J-pop ballad, while the Leona Lewis song was much, much better, but also not so different to the original Japanese song that it felt like it shouldn't have been there.