You can use the Matcher to identify identical geometries (with or without looking at attributes).
A single copy of each set of matched features is sent to the SingleMatched port, so only one of each geometery will exit this port.
@edstrat If they are an exact match - same vertices - then SpatialRelator might help. Matcher is worth trying as @geomancer suggests.
If you have a lot of data: If the stacked areas are an exact match, then you can use the CRCCalculator to create a crc code for the geometry and then just do an attribute match.
If the polygons do not match exactly (i.e. mismatch vertices) then it's a bit trickier. You can convert the areas to points (CenterPointReplacer) and then use PointOnAreaOverlayer to match the areas