The best solution that I have found is to simply remove the first line “—” from my templates and add that in after I apply the template. And since, when you apply a template to an empty document, it starts the cursor at the top, it’s as simple as typing “—” + return/enter.
As long as you don’t use the Properties sidebar or top of document stuff, it won’t re-format your document.
If you go to Settings > Editor > Properties in document {Hidden} it won’t appear at the top of the document, and you can continue to work as usual, with just a little 1/2 extra step.