This was never actually an issue. It was brought up due to a misunderstanding. All the editors agree, and have agreed for some time, about the effect and handling of auto margins on flex items, and the spec has been stable on this point for some time.
The behavior of 'auto' margins in Flexbox has changed over time. Some variants set them to zero always; others treated them as a flex of 1. The current spec completes flexbox layout, then distributes positive free space equally to all auto margins in each dimension. This has the following benefits:
The proposal is to resolve flexible sizes, then distribute remaining free space equally to all auto margins within a line in that dimension. In the cross dimension, this performs safe-alignment per item (similar to block layout) and overrides the effect of any alignment properties. In the main dimension, it distributes space amongst all auto margins in the line, allowing various grouping and justification effects.
All the Flexbox editors agree on the current model, and request the WG to officially approve this behavior.