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Obsidian fixed those problems almost by design. Instead of reiterating the benefits of using Obsidian (which can be found in almost every post lol), I'll just highlight how I personally use Obsidian for taking notes in math. For more detail, you can check out my vault on GitHub, where the README.md contains much more information, my configurations, and some sample pages (and the graph, if you're interested).
Having a descriptive yet short title for, say, a theorem, is hard without math symbols. This can clutter your links, so I wrote a plugin, Obsidian MathLinks, that allows you to associate to each note a 'math link', which will be rendered in MathJax in every note that links to it. Details and usage are in the GitHub repository.
Instant MathJax rendering!! I can't emphasize how nice this is, especially given the fact that it takes ~5 seconds to compile things in actual LaTeX. Now, even though MathJax does not have the full functionality of LaTeX, this is greatly remedied by the amazing Obsidian Extended MathJax plugin.
As for the callouts, I use the Admonition plugin! It basically enhances the native callout feature and allows you to customize it more (even custom CSS, but I haven't tried that).