I would like to suggest adding the option to make the templates that you create for a particular project to be part of (the settings of) that project. When you select the project as your active project, the "template folder" setting would be read from the Project settings and the templates would be loaded into a "Templates in current project" tab under the "New from template" option in the File menu.
That way, when you open the project and select the "New from template" option, it shows the templates that are part of the project separately, making it easy to find and select them. It also helps to prevent you from selecting the wrong template.
Additionally, these project-related templates can contain more detailed information, for example, the linked styelesheet(s) and other linked files, like a logo image etc. can be included in the template. After all, the site structure for the project is known, so linked information can be added to the template.