A Cylon Attack card is resolved in three parts:
1. Activation
2. Setup
3. Special Rule
Assuming vipers are launched during setup and Apollo is in the game, he can launch himself in one of them. He then gets an action - does it occur during phase 2 or after phase 3? The answer has a huge effect on several of the attack cards.
For example, the special rule on besieged is that 4 of the raiders immediately attack. I think that a lot of people would say that Apollo can attack them first, or order someone else to, etc. This would mean he gets to do his action before the special rule kicks in, and has a lot of far-reaching consequences.
For example, if Thirty-Three comes up and Apollo's action leads to the Basestar getting nuked, then that happens before the special rule kicks in, and thus Thirty-Three shouldn't be discarded yet. If Cylon Swarm comes up and Apollo XO's someone to jump the fleet, then that happens before the special rule happens, and thus the special rule applies to the next jump cycle.
I'm ok with these things happening, but I'd love to hear an official word on the timing.