@Yura:

Consider one thing first: In video-games, level design equals story design. The things you mention are based on visuals and equal to prequel, foreshadowing and meta-plot when it comes to story design.

The question is what you want to achieve and that should inform you on what design tools to use to get to that result.

Traditionally, a "dungeon" is site-based an either created on the basis of a simulation or it is challenge-based, potentially including back- and side-tracking to reflect that challenges and capabilities improve along the way.

In this way, story is created in retrospection by looking what has been achieved and overcome along the way.

The other thing is "dungeon as story". This too can be challenge-based but it is mainly a framing device for the overall story to be told. In this mode, if you´re not going meta all too hard, the individual rooms of the dungeon don´t really matter unless they help drive the story onward.

In this way, a story is pre-planned and just take a break when players do anything that doesn´t help taking the next step into it.