An open string is essentially fretted at the nut. Indeed, many instruments have a zero fret, therefore every note you hit on a bass is fretted. There is no difference. You're saying that every note with the kind of tapered string technology we use on a bass is imbalanced and I say that's not my experience at all. Again, I'll stress that I used SR2000 strings, where the B, E, A and D string had tapered cores, the G and C strings were "normal" and I did not experience overtones or any tonal anomalies at any point on the fretboard on any string. I am also a pedant when it comes to set-ups, for what it's worth. There are no problems with open or tapered core strings.