I would argue that being harder to extend is actually an advantage of markdown, because it helps with it staying simple and having a relatively agreed upon standard form instead of getting lost in the complexities of different ways to extend it and the different standards this would bring. Being hard to extend means that it is easier to find local optimum rather than exploring the syntax space.

Moreover, simple, human readable parsing rules help a lot with reducing cognitive load of the form and focus on the content. Extending a syntax necessarily brings abstractions and more complex parsing rules which would conflict with that goal. In some contexts minimalism and simplicity are features in themselves.

For me, I often want to spend my time writing down the stuff I need to write and not play with extensions/logic/configs. I like that it forces me to actually not be able to do sth more complex because I am pretty sure that if I was incentivised to extend it instead, I would end up spending my time with that instead of writing.

Markdown is not good for stuff where complex logical structure in the content is important to be represented in the form. In the article it is beyond clear to me why the author did not use markdown for their book, I would be more interested in why they chose RST instead of latex or another language that is more towards the complex end than the minimalistic end. I guess what the author needed was some point in-between, and they found it in RST.