I think so yes - for example if I choose the Vigier setting and plug in my Wingbass it still works but affects the way things sound, or the way the unit perceives the signal, to a degree. All you then do is set the direction of the pickup and how many strings you want to process (and if using on a five string, is the fifth string at the top or bottom of the pickup). Next you dial in the distance of each bridge point to the pickup, then adjust the sensitivity.
If I plug in my Vigier I can tune the bass however I like and it doesn't make any difference beyond the difference you'd get plugging into anything else. That's the genius of the unit IMO; it does so much but you end up taking it for granted because it's so easy to use in terms of 'playability' - once you've set it up it's as easy as plugging into any multi effect. No latency or anything like that.