Well if we're being anal about the metaphor, in construction and renovation, the scaffolding eventually goes away. Scaffolded code rarely disappears entirely; some of it usually sticks around.
It’s a little ambiguous with Entity Framework. There is no rule that says you cannot change the resulting code. If you want to continue with Code First, that is a totally valid approach, there’s even a subsection on that.
When a building is built, the scaffolding isn't an immutable part of the final product.