The mission description says that during setup, all facilities start as prepared. So am I correct to assume that this counts only for setup? So when I put down a facility card during play, it still has to be prepared, right?
In 2B, all facilities (3) start the mission in the scouted row (not prepared). From there you can retrieve them during the mission and then prepare them. All prepared cards can be used for their function, so setting these up and exploiting them is usually good in this mission.
There are currently no situations in the game where a facility could be in your deck so that you could play it from hand.