I view a mark as a compliment to your deck. With pendulums, it's a power source that you can tap in to. Yes, marks are very important and obviously must be considered in deck building, but you don't draw it, so it's not actually a part of your deck.
Notice when it says, "your deck must contain 30 cards?" That says it right there. If you have 29 pillars and a mark, you only have 29 cards in your deck. Not 30. It also says you can not have more than 60 cards in your deck. If marks were included, you'd actually have 61 cards in your deck. So, they aren't included.
And sorry, App, I misread your post.