Duplicating a track does absolutely nothing but make the same track louder. Boosting bass on one track and highs on the other track is the exact same thing as doing those EQ changes to one track and then turning it up. You guys just think it sounds better because it's louder.
I totally agree with you. You get something along the lines of a 6dB increase (if I remember correctly, I don't duplicate tracks, myself.)
The reason it's most likely "sounding better" is because it's louder, as mentioned, and you may also be cutting some frequencies where the two EQ's overlap (which will most likely be somewhere in the mids, leaving room for vocals and other instruments)
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I just can't think of a logical reason to duplicate tracks. Even if you're trying to get an effect on a specific frequency range. If the plugin doesn't have any type of filter for the effect, you could just set up a bus with a bandpass before the effect and mix it back in.
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I dunno, I guess you could sweep to find the slap range and do some sharp boosts or try setting up an exciter there. It might not sound too well though..
As for the muddy low-end... does this occur when the bass is soloed, or in the mix? If it's in the mix, try hi-passing the other instruments. Each sound (especially bass) needs to sit in it's own frequency range, otherwise they start to stumble over each other and it sounds like crap. Heh.
If it's still there when soloed, do a hi-pass on the bass until it sounds better (in the mix!) You may need to mess with the bandwidth (or "Q".) It could be due to proximity effect when the bass was recorded.
I know this topic is a little old, but I hope that helps somewhat.