The rules do not specifically state this, but when the Cylon Fleet option is being used, does the set-up for cylon and civi ships still take place at the beginning of the game or is it just assumed not to do so?

I think so. I read it as you would still start with the cylon ships actively attacking the humans at the beginning of the game.

The attack on the Colonies (Miniseries) would not have been as successful if the battlestar crews had to start responding to crises before the Cylon attack.

It says to set up the game as normal, and doesn't tell you not to put those initial ships on the board, so I guess you would include them in the initial setup just as is the base game.

I asked this question to FFG as it happens, and somewhat relevent to another thread about if Pegasus (the ship) is used.

The answer was: You set up the initial Cylon ships like normal.

Thus I say:

That follows in that the setup in Exodus happens BEFORE the Core rules (and Pegasus) happen, but do not replace them. After Exodus Setup, you continue setup for the core and if using Pegasus games.