With the old workflow, it was quite easy to rotate the environment map. The solution was to simply rotate the cube camera in fromEquirectangularTexture() before using the PMREM Generator.
With the new version of the Generator that handles the whole workflow, I cannot seem to find a solution. I guess it all happens in the equirectangular shader that is applied to the _lodPlanes. Any tips would be welcome.
If any body is interested, here is how I solved it:
The rotation shall be applied to the direction returned by the getDirection() function in the vertex shader code. I created a new uniform called angle to control it.
For my application I only need the rotation around the Y axis.