Yes, you can come back and do the Flashpoint if you decide to go to Coruscant first. You can also re-run the Flashpoint as many times as you like. When you finish it and return to the station, you can grab the quest from the quest giver both right outside the Flashpoint entrance, as well as, at the landing area for Ord Mantell and Tython shuttles.
The toughest thing in this instance seems to be finding the right door to go through. Nearly every time I've run this several people end up going the wrong direction and getting themselves lost by going up lifts when they were supposed to stay on the level, or they run left when they were supposed to run right. So just remember to check your map before you follow anyone anywhere in here. A fair number of people don't have the slightest idea where they are going.
Also, the task list above is dependent upon group choices. If in the Engineering area, the dark side option for resetting the Bridge's shields is taken, you will simply return to the command deck to face Ironfist, negating the need for destroying conduits. But this also means that you will not be able to access the LORE OBJECT which is the panel that grants you a ship codex in that area. (There is a second LORE OBJECT on the Emperor's Glory in the room with the holocom terminal where you speak to Grand Moff Kilran--it is in the area where a large droid is standing in front of a group of computer banks, there are also two smaller droids in the area. On the back side of that environmental computer bank is an interactive one that gives you a second ship codex.)
The task list also seems to skip the Bonus Quest in the area where the tractor beam is shut down. People sometimes walk past the bonus boss that is popped with you simultaneously shut down the power stations. After you defeat the boss in that room and shut down the tractor beam the robot for the bonus quest spawns on the other side of the raised walkway. (And for those first timers, without a player who has been there before. When he gets the debuff that slows him, don't be in melee range. Melee just has to sit it out, which means tanks are pretty useless in that fight and won't be the main target of the mob past the first slow unless they are troopers, who since they have a great deal more ranged damage than other tanks can sometimes keep threat, though they too can lose it.)
If you play both sides, you notice that Grand Moff Kilran is a major player in both level 10 Flashpoints.
x, 2, 2, 1, 1 - initial
x, x, x, x, x, x, x - bridge1
3 - security1
x, x, 1, x, 1, 1 - Security2
x, 1, 1, 1, 1, 2 - eng1
2, x, x, x- eng2
3 - bridge1
x, x - bride 3
3, x, 1 - elevator
2, 2 - grandmoff
3, x, 3 - sith
2, 1 - return
x, x, x, x, x - bridge4
2 - return to space station