If you set renderer.outputEncoding = THREE.sRGBEncoding and you use an EffectComposer with more than one pass to render the scene colors appear as they would without sRGBEncoding.
Here is a fiddle demonstrating the problem.
https://jsfiddle.net/cvumeLpx/2/
Comment out the second composer.addPass(renderPass); and colors will render as expected.
The second pass can be anything https://jsfiddle.net/cvumeLpx.