Axel/Lea was never being converted to a Xeha-clone thats why. On top of that its not really screwing Terra. I think itll be more Terra will be on the side of the Darkness but during the final battle Aqua and Ven will defeat/release Terra from MX's grip and by doing that one of the Darknesses will be defeated
And how does Eraqus factor into all that? Remember, Nomura confirmed that Terra had both MX and Eraqus inside him.
Also, yes it is screwing him over, because then it would make the following rather pointless:
BLANK POINTS (1ST SEGMENT, INSIDE APPRENTICE-XEHANORT'S SUBCONSCIOUS)
MX's Heart - "As I recall, you couldn't even handle your own darkness? How then will you triumph over mine?"
Terra's Heart - "Well you'll find out soon enough."
MX's Heart - "Ah, so that's how it is. Someone else has set foot into your heart. Eraqus, you sly fox."
Terra's Heart - "You're gonna get shown the door, old man."