One very important ingredient that is necessary for the <$–ENDNOTES–> marker to work is a setting in the Compatibility pane, in the compile format design interface: Flatten footnotes and comments into regular text. Without that you get “proper” endnotes, and as far as I’m aware, RTF has no way to say: put endnotes here instead of… well, at the end. So by “flattening” them we generate the formatted and numbered result of what endnotes look like, and then stick that chunk of text at the indicated spot in the output.
My Header text creates extra lines between what it thinks are paragraphs, which I have formatted it not to do (via: Format > Paragraph > Line and Paragraph Spacing).
That one is impossible to diagnose without more detailed information. A few questions that might help: What does this style look like in the Styles compile format pane? Is it present in your Format’s stylesheet? If not, how are you defining “extra lines”? Are they actual lines you could type on, or pure spacing? What else is involved in the production of the header? Is it something being generated by Section Layouts? If so, have you checked to see if there are any newlines in the Title Options or Prefix tabs?
Finally, I want to format the endnotes to match the look out of Zotero but instead…
And that, with just about all aspects of formatting, my return question would be: this for a blog, so why are you formatting anything in that case? Should you be looking to generate as clean-as-possible HTML without any formatting at all, and letting the blog software handle all of that with CSS? To me that seems more straightforward than trying to get the RTF looking like the blog software looks.
But to answer your basic question, you’d have to format those yourself after compiling. Endnote formatting, for RTF, is generally left up to how the software displays them, which in most cases will be a word processor.