If manipulating the DOM directly is so much faster than using a virtual DOM, then why do libraries like React or Ember use a virtual DOM in the first place? I honestly though it was for speed.
If you need to do something at scale, then you may choose React. The benefit here isn't from just something as simple as changing the items in a list or the text in a header, but when you need to have large amounts of state in an app that is represented by a complex DOM tree.
The benefits of React here are that the virtual DOM can prevent unnecessary updates to the rest of the tree when your state change should only affect a nested element, for example.
Being fast is not just about micro updates, I think that most vdom authors don't care too much about micro updates performance because it isn't a bottleneck.
For example, Virtual DOM with a powerful composition model can significantly reduce code size because composition gives you code reusability, and virtual dom is one of the most compact output formats to render/update DOM.