Have you read over the Evernote step documentation?
I don’t think you are quite following what the template output format setting does and how Evernote stores notes. Let me see if I can clarify…
Evernote notes are in a format called ENML, which is HTML-like. When it display them in it’s own apps, it renders this as rich text - but it is not under the hood. It’s is ENML, much like editing in a website rich-text editor that is actually creating HTML tags underneath.
If you set the template output format to ENML, you are saying that the output of that template is already creating valid ENML with tags, etc. Just like HTML, if you want bold text, you would have to be outputting
My <b>bold</b> text - just like you were writing HTML. This is an advanced feature and only suitable if you are familiar with HTML/ENML and are generating that content in scripts, etc.
If you select Markdown, you are saying the output of the template is Markdown, and Drafts runs it through the Markdown engine to convert it to HTML for you, replacing
<b>bold</b>, etc. This is generally your best option if you want to get rich-text in Evernote…there just may be cases with advanced Markdown that you are generating HTML which is not compatible with ENML…like you ran into with footnotes.