First of all, it's an independent setting. You can run it in the Third Imperium, or you can set the game in your own Traveller Universe.
You can say the exact same thing about every other Traveller incarnation plus a goodly number of other roleplaying rule systems. Rules and settings are two different things. Sometimes there's a certain connection in that some rules are unsuitable for running the kind of adventures you tend to run in a given setting, but that's all.
So far, the supplements which have to date been released don't worry about the Imperial setting. Your Third Imperium might have a Sylea - class battleship class: or it might not. Your TU might have a sully fledged Scout service like the IISS and the IGS, or it might run its Scout service more along the lines of STar Trek's Starfleet, or even the Family d'Alembert of E E Doc Smith's books.
Sure, the same rules can be used for different settings and as I understand it, Mongoose is trying to make the rules as generic as possible. And that's fine. Just as you can use non-Traveller rules for running Traveller campaigns, you can use Traveller rules in non-Traveller settings (Like, for instance, 2300AD and Babylon 5 :devil
Even within the Third Imperium setting, the year for the supplements is set currently at 1105. Characters could run the Fifth Frontier War, or the Rebellion / Hard Times / Virus / New Era, or choose to ignore all of that and just focus on a Traveller universe where things did not go the way you know they are supposed to go.
The history of a setting is tied to the setting, not to rules. Things aren't supposed to go in any specific way unless you choose to avail yourself of the setting material. If you think MGT is the greatest set of rules ever, you can use them to run adventures in Piper's Federation or Asimov's Foundation or Anderson's Terran Empire or de Camp's Viagens Interplanetarias universe or Bujold's Vorkosiverse, etc. etc.
All I care about is that, for the first time since I got involved with Traveller, a Traveller product has arrived on the market which feels like the original. No Imperial assassination, no Virus, no Vampire Ships.
The campaign setting for T20 didn't have any of that. Neither did the settings for T4 or GT. And if someone really liked the MT or TNE rules but disliked the Rebellion and everything that came after (in the history of the OTU), what's to stop them from using those rules to run adventures in the Ziru Sirka, the Interstellar Wars Era, the Rule of Man, the Long Night, Milieu 0, M200, M400, M600, M800, or M1000? (Not to mention Pipers's Sword Worlds, Asimov's Caves of Steel, Anderson's Poleosotechnic League, Niven's Known Space[*], Vance's Oikumene, etc etc.).
[*] On no account to be confused with Charted Space
.
And it's a game where the player characters' choices could determine the fate of an entire universe, if that is what the Referee decides. Not some Archduke climbing over smouldering dead bodies to claim a throne six Jump months away, and far away from the action. No. The player characters.
First of all, that's once again a setting issue; second, the scope the player characters have is exactly the same before and after the Rebellion, no matter what rules you use. If any of the things the participants of any of the CT adventures did affected the fate of a subdivision of the Imperium (I assume that 'the fate of an entire universe' is hyperbole), it was purely inadvertently and as a result of adventure writer's fiat (I'm thinking about the consequences of the event in
Twilight's Peak here).
If anything, the chaos of the Rebellion would give PCs greater scope for making a difference to greater numbers of people, as
Hard Times touched upon.
Hans