I have a SH-5 Custom in a PR CU24 SE, and a BW set in a Kiesel SCB6.
The Custom is much lower output, and therefore more dynamic. It has a lot of chunky lows, and scraping upper mids. It can be too bright in some situations. It is more mid scooped in the lower mids.
The BW Bridge is more flat overall. To me, it kind of sounds like a mix of the Distortion and Invader. It is like an Invader that has been low/hi passed for more low end clarity, and less high end fizziness than the Distortion. It is more flat overall with big bass, decent highs, and a small mid spike in the mid-mids, kinda like having a Tubescreamer on all the time. It is more compressed since it is higher output.
I like them both, and it is hard to pick just one. I think I prefer the BW, just because it works in more situations. It is just kind of a flat, blank canvas to build upon. It is like the best qualities of every Duncan, with none of the annoying qualities each model has. It is kind of bland in that way, but works well. I think the Custom works amazing in the right situation, but it is picky. It can easily be too muddy, or too icepicky depending on the particular guitar,