So I'd been playing the Sophons, and I had encountered a pretty bad bug that thankfully worked itself out later on where I couldn't progress the race storyline. Long story short, it turns out that I had gotten a victory condition before the bug figured out what was going on, so I just clicked the "Continue" button, thinking that I would get that option again when I met another victory condition. So now, here I am, having completed the main storylines, and have conquered all the other homeworlds, and am about to construct all the obelisks of space-time, and there is still no option to do that.

So, my question is, is there a way I can play the cutscene now, or did I accedentally lose that option in my vain completionist quest?

You can in the main menu open empire chronicles (Hover over Games2Gether to see it) in there all game outcomes (victories & defeats) should be saved if you go to the most recent you entry I believe you should have the option to replay the cutscene.