I would say yes.
If two sites with the same revision number are showing different features then I'd say that those features are controlled by site configuration.
As there are nearly 100 sites using the same engine it would be a support and maintenance nightmare to have different code bases for different sites. I'm virtually certain that things like YouTube support, MathJax, code prettify etc. are controlled by the site configuration. Just take these three things as an example. If it was a different code base you'd need the following versions:
- Vanilla site with no features.
- YouTube support.
- MathJax support.
- Prettify support.
- YouTube + MathJax support.
- YouTube + Prettify support.
- MathJax + Prettify support.
- YouTube, MathJax and Prettify support.
That's eight versions. Add another feature and you've got another 8 versions to support.