How about replacing the polygons by centerpoints (CenterpointReplacer or InsidepointReplacer) and then using the NeighborFinder or NeighborPairFinder to match the closest points?
That will eliminate small differences.
You can store and retrieve the actual polygon geometry in an attribute using GeometryExtractor and GeometryReplacer during the matching process.
I think erik_jan's is probably the better way to go for your current scenario, however for those interested in determining the percent overlap of features a long time ago I created a custom transformer that returned a list of all the features that overlapped the current feature and the percentage of each.
As I recall I used an AreaOnAreaOverlayer (with List), ArealCalculator then dropped the geometry and Cloned one feature for each overlapping part, promoted the attributes for that part, removed the part from the list and then exploded the list.
This gives a feature with an ID attribute (use a counter ahead of the AoAOverlayer if you don't have a unique ID), the foreign key (ID of the feature that it overlaps it) and the area of overlap.
Two features overlapping each other would produce two features A overlaps B by 30sqkm and B overlaps A by 30sqkm. Three features overlapping each other (think 3circle venn diagram) would produce 12 features: A overlaps B by 25 sq.km; A overlaps B by 6sqkm; A overlaps C by 20 sqkm; A overlaps C by 6sqkm; B overlaps A by 25 sq.km; B overlaps A by 6sqkm; B overlaps C by 17 sqkm; B overlaps C by 6sqkm; C overlaps A by 20 sq.km; C overlaps A by 6sqkm; C overlaps B by 17 sqkm; C overlaps B by 6sqkm;
These features are sent to the supplier port of a featureMerger, with the original features as the requestor, joined on the ID attribute and generating a list.
In the venn diagram example Feature A would end up with
overlaps{0}.fkey: B
overlaps{0}.area: 25
overlaps{1}.fkey: B
overlaps{1}.area: 6
overlaps{2}.fkey: C
overlaps{2}.area: 20
overlaps{3}.fkey: C
overlaps{3}.area: 6
Collapse the histogram to
overlaps{0}.fkey: B
overlaps{0}.area: 31
overlaps{1}.fkey:C
overlaps{1}.area: 26
then calculate the percent overlap by dividing the overlapping area by the area of the feature.
Thanks Eric and JDH, I will give the Centerpoints method a go, it seems fairly straight forward :)