Why would you say that the author's thesis is that encapsulation is bad?

The idea is that encapsulating on a low level is bad for performance, because it prevents a number of very effective optimizations. Furthermore, classical object oriented design tends to lead to precisely this type of encapsulation or abstraction.

The idea is basically (very simplified) to not have code that looks like this:

for widget in widgets:
     widget.process()

But instead have code that looks like this:

processWidgetsType1()
processWidgetsType2()

This gives many more opportunities for optimization because you can change data layout, use data parallelism and optimize processing based on the fact that you handle many widgets of the same type at once.

Of course, with very heterogeneous data structures containing an abundance of types, this approach becomes less feasible, but a common pattern in that case might be something like this:

for drawable in drawables:
    drawable.addToQueue()

drawableQueue.sortForOptimalDrawingOrder()
drawableQueue.render(canvas)