I totally agree muddy and dark are different things . I would equate one to the bottom half of the spectrum and one the top half. but its all subjectve terms. same as 3d, woody , smooth ,chewy
I also agree all this really depeneds on your bass players sound and how he plays . If the bass player is from the follow the guitar school then a dark sound can be great to create a massive,unified sound . but if you bass player also likes to mess with the melody allot then you really have to get out of each others way so those notes are heard .