Awesome stuff there man. This should clear various misunderstandings regarding the Emperor.
He did in the book Revan and we can pretty safely assume that it was the actual body since it was 300 years before the Treaty so the Emperor didn't depart yet. Also, when Scourge first met the Emperor in the Citadel, the Emperor showed him his mind for a split second which resulted in Scourge collapsing on the floor, crying like a baby and it involved Scourge looking directly in Emperor's eyes.
That said, it's very ambiguous as to whether the "Emperor" in JK chapter 2 finale is Voice or the actual Emperor's body since on one hand we know that Emperor left known galaxy after the Treaty and on the other hand we have a Voice in Voss body and by all accounts, there can't be 2 Voices at the same time. My personal belief is that Scourge doesn't know about Emperor's departure and that it was the Voice JK saw in chapter 2 but masked so that Voss face isn't visible. However I don't have any solid proof for that so don't quote me on that.
We don't actually know for a fact that Scourge met the Emperor in his "true" body, it's assumed by Scourge and by the reader. For all we know the Emperor could be like real life dictators who use body doubles to protect themselves from assassination attempts.
In this case the Emperor would be using a body that everyone assumes is his and not the traditional body double of someone who looks like him. For someone who is terrified of not achieving his goals and of death, I'd say it makes perfect sense for the Emperor to keep his true body hidden until he achieves his goals.
I'd be willing to wager that the only one who has actually been in the Emperor's true body's presence is Servant 2, reread the above Primer,The Problem with Scourge subsection,Servant Two, for supporting evidence of this.