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That does indeed appear to be the case. Creating a new file through applescript makes a completely bare file. I don't know why this is, perhaps so you always have the same starting point regardless of who is using the script. But there also doesn't appear to be a way to specify a template.

I believe it's possible to copy the styles from one document to another with AppleScript, I haven't looked at it in a while. There isn't a single command to do it though.