That's no contradiction since A# pins can used just like any other GPIO pin for digital purposes too.
The ADC will only be attached when needed in an analogRead() call - that's not unconventional.
But for the photo transistor vs. resistor problem, have you noticed the radio button in the hardware-examples?
When you select Transistor the text and images will change accordingly.
But sure enought, when the actual components don't even fit the cardboard schematics coming in the same box. Maybe @bsatrom can comment on that.