Today, people thinking to try markdown with dynamic contents should start with a look to Quarto. However, note that using the third way the LaTeX parts will be omitted in HTML or Word export, so this is a good solution only if your outputs will be only in LaTeX/PDF format. Therefore, you have all together the simplicity of markdown, and all the power R and all the power of LaTeX typography. The optional addition of LaTeX commands and environments directly in the markdown text (all type of commands, not only LaTeX maths).

The optional pandoc template customization, and.

The reason in that is still a markdown that can use R chunks, but in addition of some specific Rmardown/bookdown features, you can have total control over the LaTeX export via:

You have not given us clues whether you use R in your notes, and moreover I do not know Jupiter well enough to compare, but considering the above cite in the context of maths thesis, then indeed, your tool is Rmarkdown in Rstudio, and more specifically, bookdown. I am now not so sure anymore, as the jupyter-markdown loses points in terms of flexibility and things you can actually do.

Using latex in macdown