I think it has that muffled bit because (if I'm not mistaken) in the movie when that track starts, the camera shot is inside the club (normal volume). Then the camera shot switches to a long aerial shot of the EOL Club and the lights on the tower turn on (sound is muffled). And then the shot switches back again to inside the club (normal volume again). That's the only reason I can attribute it to. Maybe they lifted the track straight from the final mix of the film for distribution purposes.

After listening again closely to the copy of the "Castor" track I have, I think the actual "muffled" part was intentional by Daft Punk. I think it was just an effects layer that they liked and it fitted the tone they were going for on the track.

Now with that said, one thing I find strange about my copy of that track is that it starts out fine, but then at about the 12 second mark, it stops abruptly...then picks up again at about 14 seconds. You can even hear the echo decay after the 12 second mark, so it must be intentional. But it seems strange and almost out of place because it's such a jarring change. Nevertheless, I still love the track, jarring change and muffled sections and all!