Steps to reproduce the issue

I'm opening this issue here as response to the following questions raised here by @brianteeman so we can discuss here how to deal with them:

Its all very confusing. Writing headers to the file actually makes it more confusing (for me). Is it even compatible with setting headers for site or admin or both?

There is no way to delete all the headers from the htaccess. So once they have been written to the htaccess if you then disable that option no changes made to the settings will be applied

We also now have the situation that we have rules set in the htaccess, rules set in the plugin, and rules set in the component and no way to see in one place all the rules that are being applied. This will make debugging a faulty rule very hard.