My LBS is anti-Pilot, too. And they are a big Trek dealer.
I cannot really say what their issue is, specifically. I think they think the whole line is a "gimmick" but I don't want to put words in their mouth. They will certainly order you up one if you insist on it...but they don't stock them.
I can't really say how they stand on WSD bikes...I've seen some in the shop. I'm big - 5'9" - and fit pretty much anything so I've never really looked at them. However, I ride with one smaller woman who fits fine on her "regular" Trek 5200. The only issue she has is the reach of the STI shifter. Her hands are fairly small. Something like that could be swapped out easily with more user friendly shifters, so long as the frame/stem fits okay.
I would think with proper fitting, a WSD bike is not necessary for EVERY woman. But, I think for smaller women, I could probably see the utility.