Obsidian is very well done in general. It is a rare markdown editor for which I do not have the urge to change its default settings. However, the lack of auto-numbering is a significant drawback. I hope the developers are still working on a full MathJax support.
As a workaround, I found a solution for auto-numbering equations across Apple devices. The “One Markdown” app has both iOS and macOS versions. One Markdown automatically numbers equations as long as they are in the following format:
$$
\begin{equation}
…
\end{equation}
$$