Another possibility is that the "Faced One" entered Alii's dream and then re-injected the relevant memories into the soul of the Faceless Man, making him believe he was truly involved in the matter.
The latter is unlikely because the Faceless Man is trapped in this tower; if the Faced One could freely enter and exit the tower to make various modifications and manipulations, he would already be the "Heavens" here and wouldn't need such arrangements.
The former would mean that the two essentially are one, with one taking the larger share and the other a smaller one.
This is also why Li Zhiyuan persistently says, "You are you, yet you aren't completely you"; this is not comfort but rather a condition favorable to oneself.
Puppets and subordinates are easily manipulated by the Body, but if it's an independent part, it can be recruited and collaborated with as an aid.
Faceless Man: "You want me to help you?"
Li Zhiyuan: "Yes."
Faceless Man: "But, I'm already about to dissipate."
