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!