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The way Features is handled by Panelizer isn't quite right and prevents Features Override from working with it. Rather than just returning FEATURES_ALTER_TYPE_NONE, which disabled Override support, it needs to return FEATURES_ALTER_TYPE_INLINE and then call drupal_alter to call another alter hook.
The reason for this is that Panelizer is already using the normal CTools alter hook panelizer_panelizer_defaults_alter for it's own purposes to support Features. We use INLINE and the additional drupal_alter to provide "inline" support for overrides within Panelizer. And finally we provide the new alter hook call to Features so it knows where to export override code.
Overall, not too hard and shouldn't have any bad side effects, but give it a try. Tested it on my sites and distros here, and it's working great with Overrides now. (Patch in next comment).