I would like to know if during the preparation of a scenario there is an action window, to play stuff like Daeron's Runes, Deep Knowledge, etc

Looking at the last few pages of the rule book, there doesn't seem to be an opportunities for playing cards during setup. You actually can't play any cards until the end of the Resource Phase, so get resources then draw your 1 card then there is the first opportunity for actions.

also see page 10 of the rule book. Setup instructions are before an Turn begins. So it's not part of the turn sequence, so no opportunity for player actions. But your heroes are out and you do have your first hand (of 6) - so zero cost responses to things in setup seem to be allowed.

Eleanor FTW!

Eleanor is a response, not an action. As far as I know responses are allowed in setup, but there is no action window until the first resource phase.

... and responses must be free to play during setup, because your heroes get their resources after the encounter scenario preparation.

But your heroes are out and you do have your first hand (of 6) - so zero cost responses to things in setup seem to be allowed.

The only chance you have of playing actions during setup is if a revealed encounter card creates an action window, by giving an enemy an immediate attack.

This leads to the amusing question: are there any quests where this could happen and also the players could somehow win during setup?