Major Spoilers---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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Just realized that Young Xehanort had Yellow Eyes because Vanitas was in him… As Nomura’s interview in the Ultimania for KH3D stated Sora seeing Vanitas at the cathedral with Young Xehanort was due to Ven inside him and that Vanitas was actually there with Young Xehanort.
Of course Vanitas remained inside Xehanort since Young Xehanort picked him up and influenced Young Xehanort even after he lost his memories due to returning to his time(causing him to seek out the outside world then return to dormancy causing Xehanort’s eyes to return to their Silver color shown in the trailer for the Opening before taking over again when Master Xehanort grabbed him again).
Vanitas later gained a new body(due to absorbing the screams of Children from Monstropolis and yes this was the Major Spoiler I was talking about) when Young Xehanort was fetched by Master Xehanort and left behind enough of himself to give Xehanort Golden Eyes permanently.
I have strong suspicions that Vanitas’s Yellow Eyes and Blue-Black Hair are tied to Skuld(who has KH1 Sora’s fashion sense) since she has the same thing. In otherwords everyone is Skuld and Ventus not Sora and Xehanort!