setClearColor was not working for some reason, but found out that this property on FullScreenQuad was what I was looking for:
this.fsQuad = new FullScreenQuad( new MeshBasicMaterial( {
map: this.ptRenderer.target.texture,
blending: THREE.CustomBlending,
} ) );
The background problem is now solved.
I do however still have problems with the Reflector. Feeding a color does not seem to work for the Reflector, even though it now has a color property. I will have to debug further.
As to why I was using the encoding
property within Reflector, I was following this issue due to past performance problems when adding Reflector.
Thanks for pointing me out to the right direction.