The story will not reference side story events as having happened if the individual player hasn't played the story to "make it happen", which is why side content doesn't usually link back into MSQ, as the story can't build on something that might not have happened yet.
5.0 carefully steps around this rule because the time travel element negates the need for the player to have made those events happen at the point when the story plays out. It doesn't matter if the events of CT, Alexander and Omega are still in your future, because the Exarch has come back from an even further point in the future, so those events happened somewhere between now and then. (It's a flimsy excuse if you stare at it too hard and try to make sense of the altered timeline, but enough to scrape through.) The story can play out the same whether you completed CT or not, therefore they didn't force it.
Obviously whatever they've got planned will for 5.3 will be a different story. Something we'll be doing in the here and now will rely on the state of something changed by those events.
The obvious possibility is that we might need to wake up G'raha Tia again - which is rather hard if he was never sealed in the tower to begin with. So we would need to complete CT to ensure that has happened.
Or maybe the solution to our problem lies in the World of Darkness - and again, to ensure that world is in a particular state (Xande's covenant and the voidgate destroyed, Unei and Doga maybe still in there somewhere, Cloud of Darkness still rather furious at us?), we need to have completed CT.