It seems that the Standard Material is not using the the vertex alpha even when I run enableVertexColors() before setting the color array.
A workaround I have for now is to set the material alpha and then rebuild the material.
Checking!
Found it! You need to explicitly enable vertex alpha on the mesh:
box3.hasVertexAlpha = true;
Set it before registerScene() . enableStandardVertexColors() enables vertex colors, but alpha remains opt-in because it requires the transparent blending pipeline.
Also, the color loop should use the vertex count ( positions.length / 3 ) rather than positions.length .
Ahh, that seems to work for normal meshes, but it seems that for Thin Instances, it doesnt work.
Thanks for the updated playground!
Gosh! You’re right 
this is a separate Lite bug:)
I’ll work on it asap!