It would be nice if the Feature Joiner had the ability to scan for duplicates on the Left or Right entry point with the option of routing them through their own outputs. I think this would improve the ability to control what type of join is being created.
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Feature Joiner Duplicates
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+1If your requirement is specifically a one to one join, then the feature merger transformer might be a better option.
If you still want to use the feature merger, you can add a matcher transformer after using the feautre joiner to see if features are duplicates and decide how you want to handle these records.