jseth,
If using Windows Deployment tool kit is the easiest option for you to get your base image setup and configured the way you want it there isn't any downside to doing that. Mirage will simply take the Base Layer you create on the Reference machine and use it.
As far as if you should remove it from the domain prior to deployment, no you should leave it joined to the domain, this also lets you make updates later to the base layer which you can deploy as an update to the base layer.