Somewhat related to #268
The problem appears to be with the merged mesh code path (animated: false), it then only uses the theme colors.

I don't think three would support separate coloring with the BufferGeometry, except maybe using far more advanced material application?
Maybe an option on GraphScene to override the codepath even if animated: false would be an alternative until a better solution comes along (with a quick note that this is at the cost of performance optimization - but for smaller graphs, should be fine)?