Ok, so how I interpreted it is... Steven and Marc put their heart on the scales. 2 hearts for 2 egos. But since we were missing Jake, it wouldnt balance. But then Steven fell off the boat and essentially became "nothing" in the Duat and so the scale balanced with 2 hearts, 2 egos. Steven's heart didnt just disappear from the scales the moment he fell off, for example.
The loop or plot hole in that situation, is that the heart that was now standing in for Jake is being judged and not Jakes actual heart. Jake could be a pure evil, murdering gangster, and could have walked into the Elysian Fields. I figured a future plot point was going to come out of this, but.. I guess its just sand under the rug. That or its something theyre sand bagging for later.
As far as Khonshu and Jake, I imagine khonshu will manipulate the world around Marc/Steven so that theyre always Triggered into letting Jake take control. The future plot point is probably where Jake is in control so much now, that Steven or Marc is eventually going to figure it out and then we'll see some type of inner struggle for control with no actual result (cause that doesnt make movies/series).