There's no reason why JSX had to be included at the same time with React. There's no reason for it to provide classes, the whole bells and whistles.
They could have released just the Virtual DOM part of the library (which was the major innovation) and keep other parts of it to themselves or release them later. When React released with so many features at once, it looked on the surface like just another framework. In fact, people still call it a framework today, even though it isn't one and was never really meant to be one.
And the fact that React was released in a such a big package, it meant that people weren't eased into each of the concepts, one at a time. Suddenly you not only have to learn about Virtual DOM, but the class API, JSX at once. Some people even throw Redux at the junior programmer at the same time. Imagine having to learn so many concepts at once! No wonder it's hard to learn.
It's a pretty basic pedagogical concept. You have to introduce each concept in isolation and then build understanding of the whole from those parts. If you do not understand what the problem with vanilla DOM manipulation is, there's no rush to learn JSX and Redux!
I guess in the end I'm just glad you decided to play around with vanilla DOM manipulation and build from that, step by step. "Learn everything at once" doesn't work very well.