DS3 is not compatible with regular PCs (natively at least) yet they played Watch_Dogs with one on a PC at last years E3.
One thing I think people forget, these guys are game developers, coders, engineers. I don't think it would be very hard for them to make a DS4 work with a PC.
I think that's a bit too much effort to put in when they can easily get a 360 controller or a xbone controller. I think it's running on a dev kit unit for PS4. That explicit show of controller for a time that long was unnecessary unless they wanted to highlight the platform.
As for WD's last year reveal I don't recall any PS controller. And lest we forget Ubisoft and Sony seem to have a some strategic partnership (much like Activision had with MS this gen).