I have now found a different way to solve this. Because whenever the main hfs template is used, the header is sent, but when my .html file is used it isn't, I have moved my home page to /index.html, removed it from / and made / non browsable. This means that visiting the root of my website returns a 403 error. I then put a html redirect in the hfs template to my /index.html file.
This is probably a really bad way of doing this, but as long as I don't get 403 errors for any other reason it should work.