How this Site is Made
I write everything in html (except when I don't) and store entries as a (simple) but complete HTML document. I've used Markdown with Hugo and TiddlyWiki and variouse applications. It seams that I've always had to use HTM inside Markdow to get the formating or effect that I needed.
An other benefit of using HTML as your data format is that it will probably last for ever. There is no silver bullet and if you are going to use HTML you have to have a good editor and understands HTML. I use Vim. There are many plugin for vim but I've had good luck using the xml-plugin for vim.
I guess it's obvious that you have to know HTML to use HTML as your data format but in the "long run" I think it simplifies your development stack. You can only keep so much in your brain and if you are going to create for the web you will have to know html.
Xquery and Basex
In my world I am mostly reading, collecting and creating documents. The Web is built on documents. I think Xquery workes a well as any other language I've used (php, python). Basex provides an interpretor for Xquery, a database for storing html and an application server for xquery apps. The use of html, xquery, xquery database really gives you a great platform for creating your website. None of this is easy! Peter Norvig has a great article about learning almost anything, but in particulare how to program. Teach Yourself Programming in Ten Years