Comparison comparison = EMFCompare.builder().setMatchEngine(new DefaultMatchEngine(DefaultMatchEngine
		.createDefaultEObjectMatcher(UseIdentifiers.WHEN_AVAILABLE), comparisonFactory)).build().compare(scope);

public class MyMatchEngineFactory extends MatchEngineFactoryImpl {
    public MyMatchEngineFactory() {
        super(DefaultMatchEngine.createDefaultEObjectMatcher(UseIdentifiers.WHEN_AVAILABLE),
                makeComparisonFactory());
    }

    private static IComparisonFactory makeComparisonFactory() {
        return new DefaultComparisonFactory(makeEqualityHelper());
    }

    private static IEqualityHelperFactory makeEqualityHelper() {
        return new DefaultEqualityHelperFactory() {
            @Override
            public IEqualityHelper createEqualityHelper() {
                final LoadingCache<EObject, URI> cache = EqualityHelper.createDefaultCache(getCacheBuilder());
                return new EqualityHelper(cache) {
                    @Override
                    public boolean matchingValues(Object object1, Object object2) {
                        // My custom code
                        return match;
                    }
                };
            }
        };
    }
}

   <extension
         point="org.eclipse.emf.compare.rcp.matchEngine">
      <engineFactory
            class="my.plugin.MyMatchEngineFactory"
            label="My Match Engine"
            ranking="20">
      </engineFactory>