The reason we start from a fresh OS install into a VM for the reference machine is to keep it as free of hardware information as possible. This allows us to ensure we can then then deploy that image to any target hardware. We don't support starting from a physical machine, or P2V, because we can't guarantee the state of the deployed target machine.
For example, one could P2V a Dell OEM machine, which would have an entire set of drivers installed for that particular machine, and perhaps other Dell models, as well as model or manufacturer specific software. One could argue that we could go in and strip all of those drivers out, and while it might be somewhat possible, it could never be 100% accurate.
We want to ensure that only the exact device drivers from the SmartDeploy platform pack for the target device are used, and that the deployments work as cleanly and as reliably as possible.