I don't think it's just Windows that encourages x86 use; it's also the fact that the ecosystem is richer for that chipset anyway (hardware compatibility for things like the webcam and card reader come to mind). If you decide to go with a linux distro on top of custom hardware, then you might have to develop drivers yourself, as well as build up some UI paradigms customized for touch. WebOS gives them a great starting point to do just that, so in the end their actions still look consistent with their goals.