PostGIS: Cutting Holes in Self Geometry
I was able to achieve a sub-optimal solution with the help of Craig and Alexandros in the above comments.


Identify which polygons are children, and flag them as such:  

UPDATE zones a SET parent = b.id FROM zones b WHERE ST_Contains(b.geom, a.geom) AND a.id != b.id;
Perform two queries in TileMill for both parental, and children geometries

Parents:    (SELECT * from zones WHERE parent IS NULL)
Children:(SELECT * from zones WHERE parent IS NOT NULL)
Apply a comp-op to the parental layer only and ensure that the children geometry layer is "above" the parental one in the layers list so that it is draw on top.


Unfortunately, this is still not perfect. Children geometries still cannot have an opacity value, otherwise the parent color will blend, and cause it to take on another color.