I have a general scene where I'd like to show different kind of models. Depending on the source of the model sometimes the model contains MeshPhongMaterial, sometimes MeshStandardMaterial, and sometimes both of them.
I also have a specific lighting model with an AmbientLight, and a DirectionalLight that points always to the same direction as the camera, so you will see clearly what you are looking at right now.
To make MeshStandardMaterial look better I've also added an environment map to the scene (not the materials), and I was pretty satisfied with the result.
Here is the result with r130 (Phong material on the left, Standard material on the right):

After I update three.js to r131 the result looks something like this:
I understand that environment maps are auto-converted to PMREM from r131, and this causes the change. I also understand that this is more correct than using non PMREM environment maps, but now it messes up my scene.
On some other topic it was recommended to remove ambient and directional light (because lighting now comes from the environment), but it results in this:
Now the object with standard material looks fine, but the object with phong material is completely black. I've also lost my previous feature that the directional light always points where the camera looks.
By removing ambient light only I get this (still not what I want to achieve):
So basically my question is: Although I know that this is not physically correct, is there a way to apply an environment map that doesn't affect the lighting of the scene, but affects reflections of standard materials?
Here you can find the code of the mentioned scene: https://github.com/kovacsv/Online3DViewer/blob/dev/sandbox/three_envmap_issue/three_viewer.html
And here you can see it live: https://raw.githack.com/kovacsv/Online3DViewer/dev/sandbox/three_envmap_issue/envmap_issue.html
So basically my question is: Although I know that this is not physically correct, is there a way to apply an environment map that doesn't affect the lighting of the scene, but affects reflections of standard materials?
No, there isn't. MeshStandardMaterial and MeshPhysicalMaterial require now a more strict PBR workflow. As you pointed out correctly, your previous setup was physically incorrect. This has been fixed and there are no plans right now to allow previous workflows again. Environment maps are considered to be used as IBLs. So conceptually they always affect the lighting no matter how you parameterize the material.
The solution for your use case is to a) use phong materials or b) update the lighting of your scene and accept the new style.