is a template I can use out of the box by just dropping in my content and configurations, rather than designing or building myself
is not feature-poor. I want it to have features like footnotes, jump-to-section links, citations, on-hover pop-ups for citations or footnotes, syntax highlighting for code blocks, etc.
nice to have: ability to draw basic graphs or diagrams (helps in technical explanations)
is not too difficult to customize by editing the code directly, Customizing the looks, structure, or adding functionality if I needed
Programming language doesn't matter much. I can use whatever. I do have a preference for functional languages.
Eleventy seems like a great framework to do this, but as I said I want a template that's ready out of the box not just a framework. The blogging template I found for eleventy does not look as nice as I hope.
Have used Hugo, and I don't really know what you mean by 'not very easy to customize client side code'. Hugo works with 'themes', which you can either download online, or create yourself. Customizing CSS, JS and even the HTML structure can easily be done by modifying/patching said theme.