For anyone else hitting this wall like I was, I created a Shader based video player in 8th wall, using aframe which is removing background using an alpha map in real time, but I was having ridiculous sorting issues on my end not resolving even though the logic was sound. Anyway, this solved the problem above. Thank you.

Explicitly setting the sortObjects to true is key.

Either

<A-scene renderer="sortObjects: true">

or

document.querySelector('a-scene').renderer.sortObjects = true

Cheers for the fix.