Hi Grant,
I don't see a simple way around that to use the template and a different domain (or subdomain) at the same time.
I will drop a note to Scott to see if he has anything to add. He is travelling so don't expect an immediate answer.
Personally what I would do in a case like this is to use the template on the standard dnndev.me domain initially. Then I would copy the generated project over to the subdomain site, open the .csproj file for the project and replace the dnndev.me domain with the subdomain you want.
Cheers,
Aderson