Sorr that you're running into this issue. I'd assume that the create from template method works the way you expect because the template you are using has the UTF-8 set in the code. We are using a built in Dreamweaver call to create the new pages, and it appears that that call doesn't respect that setting in the preference dialog for the encoding to use for new documents.
I'm sure that this will be an issue for a couple of other extensions that generate pages. I'll log a bug and we'll see if we can determine the encoding selection and use that if possible, else we'll need to minimally document this issue.
Thanks for taking the time to investigate the issue further and letting us know about the problem you're having.