My girlfriend plays bass and she told me that the reason you don't hear much alt-tuned bass is because bass usually is used for the purpose of holding down the rhythm or holding down the melody (like Joy Division) and therefore most bands use it simply for that purpose, and it would be distracting if there was an alt-tuned bass in the middle of the other instruments.
I guess that's true, even if it's a bit obvious of an answer.
The more I thought about it... I think Girls Against Boys used alternate bass tunings (they had two bassists also).
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