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.
The earlygame will be all about farming. After hitting Level 6 your Armor and Magic Resist are already higher than they would be with flat runes.
About the Marks: It makes you weaker in Earlygame, but even with only one Zeal and nothing else it will pay out instantly. Also, with IE this will compensate for exchanging high-damage items for more Crit and AS.