Not Updated For Current Season
The masteries shown here are not yet updated for the current season, the guide author needs to set up the new masteries. As such, they will be different than the masteries you see in-game.
I think that the runes on the AP is not worth collecting because they are very weak. And when assembling the runes on the CD you get a useful result. Another necessary thing for Lux - Mag Regen, so we take the blue runes exactly that. Well, is a slot for red runes. For those un the most useful are the runes on Mage Pen.