Hi i can answer this one as i have the rule books right here in front of me.
Answer: Pegasus rules takes precedence in this and regardless of whether the current player or the CAG is instructed to place civillian ships
Exodus rule book p22 : Note that during the New Caprica phase, civilian ships are utilized as described on pages 13–17 of the Pegasus rulebook. Civilian ships do not remain in space areas during New Caprica setup. However, after Galactica has returned to orbit, vipers may be activated to escort civilian ships in space areas as described on page 15 of this rulebook.
Exodus rule book P14: Whenever a game effect instructs the CAG to place a civilian ship on the main game board, the CAG chooses which space area to place the ship in. The CAG must, if able,* place the civilian ship in a space area that does not already have a civilian ship in it.
* Note the Cag is 'Not Able' to do this because the rules in pegasus stipulate how the ships are placed
Pegasus rulebook p15: During the Prepare for Jump step of every subsequent New Caprica Crisis Card, when an evacuation icon appears, the current player takes one civilian ship from the top of the Prepared Civilian Ships stack and moves it to any space area with a viper launch icon.
the FAQ also resolves the issue: as a specific area is indicated by the Pegasus rule book.
Q: When a game effect instructs a player to place a civilian ship in a specific space area, such as behind Galactica, does the CAG choose a space area instead?
A: No, the CAG only chooses where to place civilian ships only in cases where no specific space area is indicated.