As explained in the link, Vega uses many of the D3’s geometry and other utilities, but not the DOM manipulation that most people associate with D3. So the laye

As explained in the link, Vega uses many of the D3’s geometry and other utilities, but not the DOM manipulation that most people associate with D3. So the layers are not even in this comparison - Vega is sort of on the same level as D3, and Vega Lite vs Observable Plot is a better comparison.