I have been fortunate to get backstage with a handful of famous artists, like on the G-3 tour, etc. I asked the techs if there was anything special about the pickups those guys use and they said that they are not 100% the same as the off the shelf versions everyone else uses. Most of them are hand made for each artist. Of course this is not the case with everyone, but the information didn't surprise me.
If you check out the "How we make them" page on BKP's homepage it gives a pretty good reason for scatterwinding. Compared to moset other pickups it does add a tremendous amount of clarity to the pickups. I noticed a lot of people comment on how every note in a chord rings out well, where in some pickups they mud up or smoosh together under heavy overdrive (Dimarzio in particular). There is definitely a higher amount of treble to BKPs, but this is controllable with an amp and varies greatly between pickup models, as well as guitar woods.
Because of what a lot of people listen to their ears are trained for a certain tone and are use to SD, Dimarzio, EMG, etc. It's familiar to them is all. However, little by little everyone is seeing a lot fo credible artists jumping on the BKP wagon, which is awesome. It's all about personal taste though and I'm sure there are plenty of people who do not dig the BKP sound. I tend to find people who have good or perfect pitch and a discerning ear for tone gravitate to BKP or some custom pickup tone as apposed to mainstream, off the shelf stuff. All of my guitars with BKPs sound immensely better, and against other brands they really stand out showing more dynamics, harmonics, etc. But, don't forget that most of your tone comes from your own hands. Maybe there's something to go with the idea that uniquely wound pickups complement each person's unique hands and therefore their tone.