I read your thread and perhaps I'm not understanding you. You might be better off writing steps to repro. Anyway what are you ultimately trying to achieve?
It looks like when you create a new project you are wanting to load a custom template by default. If so rename the template and set that as default.
If the wrong template is being loaded by default select the correct template and then press the 'set as default template' button.
If you are using template filenames that Sonar uses the chances are it will be overwritten, so obviously don't use the template filenames Sonar uses!
Or am I misunderstanding?