This feature is planned to be removed from this plugin, and instead, it will be available as a separate plugin Better Math in Callouts & Blockquotes, featuring a bunch of improvements. Currently awaiting for approval by the Obsidian team.
Obsidian natively renders
> $$
> \begin{align}
> a &= b \\
> &= c
> \end{align}
> $$
With this plugin, you will no longer have this nightmare!