> Since most artists probably start with a composition in the 2d space of the artwork, there’s never really a coherent 3d space to place the light sources in or figure out those projections in.

Highly skilled artists don't just think in 2D — they really do imagine the 3D scene that they're painting. It's hard to relate to but people with a lot of drawing/painting experience can "feel the form", as they say, when they draw. But it's true that figuring out the lighting is still difficult even then.

I do want to point out that if you look at talented painters from later in history than the early renaissance, they don't make nearly as many mistakes as the ones in the article, although of course the lighting of imaginary scenes is still always approximated and simplified.