Er... Destroy wrecks the Citadel - Destroys it, pretty much. Plus no EDI and I don't Joker's gonna be in a partying mood. Not to mention allllll the bodies and destruction, how are you gonna make that sync up?
Hackett confirms in the destroy epilogue that the Citadel is rebuilt. It goes from this;
Re EDI, we have no idea how the Crucible beam works in relation to synthetics other than it doesn't outright physically destroy them. From the Citadel DLC we know that EDI can be shut down. If EDI shuts herself down as the Normandy's being chased by the beam, what happens? Besides, this is on the basis that the Catalyst is even telling the truth to begin with. When presenting the choices to you, and from his reactions when you choose, it's clear that it wants you to pick either Control or Synthesis. It mentions the destroy option because it knows that you already know about this anyway, but then tries to put a blocker on it by saying that there's a downside, ie. ALL synthetics die. That might be true, but he's hardly going to sugarcoat it either way. "Yes, here's this option to destroy us, and there's no downside at all....wait, don't you even want to hear the other options? No? stop! Wait!"
I can mentally justify EDI surviving the destroy ending, either by shutting down, or by the Catalyst talking b*llocks.
Plus, why should you have to pick Destroy to get to play it?
It's your reward for choosing wisely.....
Or seriously, the first half of the mission can be completed in-game prior to Cronos Station - the latter half, particularly the party, can be after the end of the game. If Shepard survives via Destroy then it's set after the rebuilding some time later. If you pick control or synthesis then it's like the Church scene at the end of Lost - Shepard's final thoughts playing out as a final goodbye with his/her friends.