I created a template from an existing project but it didn't faithfully represent the original project in one important way: the original project had Issues and Meetings features turned off, but the template didn't disable them. I had to edit the template to turn off those tools.
After a discussion with support this is not a defect. When creating from an existing project you only decide first which content from the project it is that you want to be added to the new template. I can agree that this can be confusing that the settings for which tools are turned off are not copied into the new template. However later this year we plan to update the templates and this idea will work as an input to that work.