I know it seems like a pain in rear, but for some people this feature is a blessing.
However, I am not one of those people who think it is a blessing

.
But we have to respect others ways of working just like they would us.
What I do is delete all the content by selecting - right click lasso.
Then press delete special. Then save the template as a different name. Incase something happens you want to be able to load your original project.
There's nothing worse than deleting all your tracks and then accidentally saving it as a project instead of a template.
That's why im not a fan of this. I would like to see (probably like you) a fail safe way to save templates that doesn't include projects.
There is debate though that project templates were never made to be used like that.
I typically set up my templates from scratch.