A lot of Elle's abilities like her Action Girl status and Inexplicably Awesome martial arts powers become this once you discover Niander Wallace Junior is her creator. It seems very likely that he arranged everything to assassinate his father and establish his control over the company. It also explains Elle's rebellion and that she might not have Heroic Willpower after all.
While a friendship was implied in previous episodes, Joseph sparing Marlowe in "Free Will" makes more sense when you see that Marlowe went out of his way to protect Joseph when the latter refused to terminate a Replicant.
We never learn the name of the Replicant that Joseph falls in love with during "Clair De Lune" (except in the credits, which list her as Selene). Which seems like an oversight until you realize it's very possible that Joseph never bothered to learn it or deliberately kept himself from doing so in hopes of keeping his emotional distance.
It seems a Contrived Coincidence that Niander Wallace Junior would pay Joseph to look after Elle. There's no way that he could have known that she would go to his building. Except, we know that Elle was programmed with the building's location. Which means Niander Wallace Junior always knew what was going on.
Niander Wallace Junior tattooing another beautiful Replicant woman with a different species of flower in "Clair De Lune" pretty much establishes that Elle is just one of many. Given we saw his The Dragon in Blade Runner 2049 was Action Girl Luv, it seems very likely that he has a fondness for this kind of minion. Worse, he seems to train them to all love him.
Due to Foregone Conclusion, Niander Wallace Junior is not going to suffer any consequences for his actions barring possibly losing his eyesight and will become one of the most powerful men in the world.
