Before taking up bass I used to mess around a lot making techno music. One of the most common experiences/problems is making a great, unusual sound, but then finding it difficult to get it to 'sit' in the track you're writing. Sometimes with clever processing and mixing skills, you can twist it in, but it's often very hard. I'd go as far to say that most sounds don't work well together, and when people find a combination that works they tend to milk it for all it's worth - which is why, despite the infinite possibilities available to you when writing synthesized music, most tracks fall into a few recognisable styles with sets of sounds that work well together.
By the same token, acoustic music has recognised setups - the string quartet in classical, the piano trio in Jazz... and for amplified music, the classic drumset, clean(ish) bass, one or two distorted guitars, and vocals is another setup that works...
.... Stick the cymbals in and two guitars that weren't Heavy sounding either, and the great sound was lost in the Mid to high mix.
So... distorted bass and quite clean guitar didn't instantly seem to work so well - at least in the track you played. But there's so much you can change - EQ, ambience, playing technique, levels - you can probably get most effects to work with most songs, if you're prepared to tweak every instrument. But if messing with sounds like that doesn't interest you that much - it's true, why bother? At the same time, for some people messing around with sounds is the whole point... the songs are just an excuse...
My conclusion: if its Bass you play keep it bassy!
in some styles, sure... other times, it's the bass drum that holds down the low end, and the bass is free to be percussive, melodic, chordal... places where effects might work better.
But again, i think I know what you're saying - how many classic basslines (of any style) are played by really complex sounds?