First, that tutorial was interesting and useful. But I don't think that CSS is supported in kindle https://www.amazon.com/gp/feature.html?docId=1000729901 or epub. I could not even find that css in the epub3 support grid http://epubtest.org/features/ (which may or may not mean something). That sounds like the sort of thing which Google Play Books MIGHT support though I'd want to verify.
Second, my method for producing epub accomplishes exactly what you want. I am using Docbook XML (and Docbook XSLT) to generate XHTML output which I then zip and validate. It's not an easy solution and it is very tricky, but Docbook has much more semantically rich elements and some powerful ways to style it. It includes various different methods for changing the numbering for sections (and even omitting the numbering). It also has different methods for chunking the output by chapter/section/subsection.
Unfortunately documentation for producing epubs is not up to date. (In fact, it just occurred to me that I should write up a tutorial about my own process).
While Docbook may require too much learning curve for your current task, its approach illustrates how to solve the problem in another way.
With regard to your specific need, I think it's perfectly valid to hardcode numbering into your sections -- even if it will be hard to maintain over time. Sometimes the dumb solution is still the best. You could use a media query to separate between reading systems that support the css and those that do not. (But that could be messy if you need to change the content and not just the presentation).
This raises another question. Wouldn't you want the TOC to reflect the numbering as well? Yes, it's possible to have different levels in your TOC. The excellent book Epub3 Best Practices by Matt Garish covers topics like that -- although it doesn't go into detail about css support -- which is still a moving target. (I suspect that Oreilly is also using Docbook behind their production process as well)