IComparisonFactory comparisonFactory = new DefaultComparisonFactory(new DefaultEqualityHelperFactory() {
    public IEqualityHelper createEqualityHelper() {
        return new MyEqualityHelper();
    }
});
IEObjectMatcher matcher = DefaultMatchEngine.createDefaultEObjectMatcher(UseIdentifiers.WHEN_AVAILABLE);
IMatchEngine customMatchEngine = new DefaultMatchEngine(matcher, comparisonFactory);

IMatchEngine.Factory engineFactory = new MatchEngineFactoryImpl() {
  public IMatchEngine getMatchEngine() {
    return customMatchEngine;
  }
};
engineFactory.setRanking(20); // default engine ranking is 10, must be higher to override.
registry.add(engineFactory);
EMFCompare.builder().setMatchEngineFactoryRegistry(registry).build().compare(scope);