Printing the filament like in the linked article is essentially in 2D (not really, but for this point it's close enough). So if you have 2 colors, you can first print all color 1 segments, and then manually switch and print all color 2 segments.

In a real object your print is 3D and consists of layers that are ~ 0.1-0.2mm high. In a typical multicolor print each layer has several colors, and you have to finish a layer before printing the next one. So you have to switch between all colors that are present in each layer.

To create the 'programmable filament,' you only switch over to each color once as they generate the toolpath in such a way that the nozzle doesn't interfere with previously printed filament (and the printer resets the z-axis back to 'layer 0' each time it switches colors).

For making relatively small, multi-material / multi-color prints, this really is a pretty clever system that looks reasonably practical on a wide variety of existing low-end 3D printers. With good software support, I could imagine being able to make things with interesting physical properties by making hybrid rigid / flexible materials (integrated hinges or other deformable parts, for instance).