some people still think its stupid how he could've been crushed by a boulder but his eye survived Lol
explanation: His eye's ability is to phase / go into another dimension s/t jutsu. He was apparently unaware of his ability back then and did it without knowing (maybe) . After the boulder hit his body, his eye must've went into motion with the phasing ability so his skin on the outside was crushed but his body wasn't crushed on the inside too soon before it was sent to the other dimension. His eye is in his head so it protected things in that area first (on the inside) .
His eye holds the ability itself somewhat so the eye phases first, then the rest of the body can.

OR Zetsu was already planted inside Obito; came out to protect a portion of the crushed half of his (obito's) body. Or while Obito's body lie under the boulder, Zetsu quickly moved into place of his right side and began fusing with him in away , somewhat just similar to how he snuck up on and appeared in the Kage at the summit.