The Clausewitz Engine stores every possible variable in an xml format so it should be very easy for the developers to implement any kind of Star Trek canon events with various alternate outcomes depending on player choice. Historical grand strategy titles using the same engine had very popular game mods that tried to offset the very random nature of the game by adding tons of historical events like the French Wars of Religion, the English Civil War, the War of Spanish Succession, giving options for the player to influence historical outcomes of succession crises or decide which side to join in a civil war, complete with alternate royal lineages up to the end of the game. If there's a variable governing it, an event could be written for it, with all kinds of conditions governing whether it gets activated or not.