Two issues here.
First issue is with the procedural generation of the universe. Here's how it works, as I understand it. First, the overall shape of the galaxy is laid down in a "cloud" of mass. Stars are condensed out of this mass, according to the star-generation algorithms. This process only crudely imitates how actual stars are made in an actual galaxy.
Once you get down to the individual star systems, the star system algorithms run a rough simulation of events that happen - including random events like rogue planets and stars wandering through the system, disrupting orbits. The actual planets aren't generated and positioned at this stage, it's all just probability clouds. The next step is actually generating the planets in their orbital positions at time=0, which is presumably midnight on January 1, 3300. Finally, time is fast-forwarded to the current game date to generate the planets in their correct locations. All of this happens during the "loading screen" cleverly disguised as a hyperspace jump. It's also doing other stuff at the same time, like calculating what the skybox of background stars looks like and checking to see if there are any other player-inhabited instances in the system it can insert you into when you arrive.
The main problem with "time travel" here is that "time=0" thing. You can only go back to zero time, I don't think you'd do well trying to go into negative time. So you couldn't go back to 3250, or 2375, or 2019.
The second issue is that this game is of course multiplayer. In a multiplayer game, everyone must run on the same clock. If ED had a single-player mode, then sure, time travel all you want. But it simply can't happen in multiplayer, unless every single player gets time-travelled simultaneously, otherwise the number of parallel universes the game needs to keep track of multiplies very quickly.
Example: I've worked hard to put "my faction" in power in a certain star system they have invaded. You decide you don't like this state of affairs, so you go back in time to before my faction invaded the system (this in turn requires ED to "remember" the past history of the game - something which I'm pretty sure it isn't currently doing), and you either prevent my faction from Expanding into the system or you fight back to kick my faction out of the system again. It should be easy, because I won't be there to oppose you, because I haven't gone back in time.
We now have two separate timelines the game has to keep track of - two competely separate universes, one where it's still the present and my faction has won (because I'm still there in that universe and still supporting my faction) while in your alternate-history universe, my faction (and me) isn't there. Now, multiply this by the number of times every player in the game ever uses time-travel. Each time, a new universe is created. FD would quickly run out of server space to hold all those universes.
