I think this actually make sense. My anim loop was calling a routine for capturing 3D scene from all probes: problem is the render call was after that routine, thus after the transform resets. Maybe this could be possibly improved if the pmremGenerator.fromScene() has a direct call (or option) to render before performing the capture.
So the problem is mainly on pmremGenerator.fromCubemap() that still exhibits mirrored capture on x axis (see sphere sample screenshot)