When using vertex parenting, an option for using the parent object
final evaluated indices is exposed in the Object Properties: Relations
panel. This allows the calculation of the parent vertex position to
ignore the the CD_ORIGINDEX layer and instead use the final indices
that may have been altered by the node tree evaluation.
The indices that will be used for the vertex parenting are also exposed
to the UI in the same panel, allowing them to be altered after the
vertex parent has been created.