You've got a good ear. ;)
I debated with myself whether to delete that sound effect or not, since it is certainly a 1997 addition created by augmenting the low end of the deceleration effect, which was originally only present in the mono mix. But in the end I decided to leave it, since it was a relatively small thing and I do like the way it sounds. (The deceleration effect is the one of the only things about the mono mix that I miss in the others.) Since the LFE channel as a whole is pretty much a 'best guess' of what it could have been, I figured I could give myself a little leeway in that case.
In the 2004 mix, that bass effect is presented at much higher volume, which sounds really cool and is one of the few things I actually like about it. While I would have liked to be able to use that one, I couldn't justify it being that loud when I knew it wouldn't have sounded like that originally, so I compromised by going with the more subtle '97 version; and also the '04 didn't have the other impacts that the '97 did. (Both of them have the high frequency sounds of debris whizzing by the ship, which were first heard in the '93 mix, but in both SE's they seem even higher-pitched, and are timed and panned differently than the '93.)
On a low-fi subwoofer, which most mass market products are, the descending frequency sweep could be indistinguishable from a generic rumbling anyway. Like a lot of things, I guess it depends on individual preference, equipment quality, and listening ability for whether it works or not.
How did you like the bass in the rest of the movie?