I'm sure that was not a "production" issue, but more of a "mixing" issue. Sure, JM put the "distortion lol" effect in his pedalboard and MP said "lol heavy, balls cool! we're staying with that", but with proper mixing bass (Distorted or not) can compliment guitars quite nicely, like Train of Thought for example.
Unless I'm remembering the making of Train of Thought videos completely incorrectly, I don't think the bass on ToT is actually very distorted, if it's distorted at all.
Having a lot of distortion on bass can work (Trujillo's bass on Death Magnetic is super distorted but sounds great on the Guitar Hero mixes), but on BCSL it didn't. It's not really a mixing issue either. On the unmixed Wither and TBOT demos you can't hear the bass worth a damn. Maybe it could have been saved in the mix, but my inability to achieve any results with the stems is highly discouraging.
Yeah, JM shouldn't have thrown that tone on his bass, but it is kinda a producer issue. JP and/or MP should have said "hey, wait a second, I can't really hear the bass. We need to do something with the tone." But JR said before the album was released that the bass sounded better than ever, so that should say quite a lot of things about how DT approached their sound at the time. Hopefully now it's different.