When I say plain text, I mean plain-text. I mean not even markdown. Just plain text. The client can choose to make links clickable if they like.
Any formatted document should come as an attachment (I'd prefer PDF). I guess it should be an attachment I expect or I probably wouldn't open it. In any case, I don't like emails with tracking. It feels forced. If you really care, send delivery and read receipt requests but I doubt we do.
Markdown should stay where it belongs. It should convert into HTML in the server, not on my client.