Does this prove or disprove anything? Wily having begun construction on Zero while Mega Man is still running around proves X is a separate robot from Mega Man. At least, that's how I've seen Bass' endings used in arguments. I was always under the impression that Zero's purpose was to destroy X from the very beginning.
Flame posted the videos in response to:
"I'm pretty sure Zero was made specifically to destroy X, right?"
Rock being X or not is a separate discussion. One to which we already have a clear undeniable answer.
Wily in Zero's dream in X4 is talking about X .Wily: After him! He is my nemesis. Our rivalry is what gives me motivation in life. Now go!
Destroy him! That's an order.
"Him", "He", is in reference to Rock or X. "Our" to Dr. Right.
In regard to whether Zero's goal is to defeat Rock or X;
-The arcade games say he's to destroy Rock, Bass and take over the world.
-X3 says X knows his destiny is to do battle with Zero.
-X5 says Zero forgot what he must do (when he turned good), until he awakened and concluded he must destroy X.
As Hypershell said, there's a clear shift of focus - first and foremost because Zero never took over the world and instead was sealed away with a cognitive flaw.