I use hugo with the book theme (https://github.com/alex-shpak/hugo-book). It takes a bit of getting used to (if you're not familiar with hugo) but after that it's pretty good with all the flexibility that hugo provides for shortcodes, etc. You can get auto numbering of figures, equations, etc. with appropriate shortcodes. Is it possible to get autonumbering in mdBook?

It also gives a nice toc/tags on the right side (if you want it), and the ability to split the page into columns. The katex support is good (looks like mdBook uses mathjax) and publishing is easy and is just a push/rsync.