Is it possible to modify the DopplerFactor in Edit->ProjectSettings->Audio on-the-fly per scene?

For various reasons, we were forced to use individual scaling of our scenes, so several scenes are no longer in Meters. However, the Doppler Factor in Edit->ProjectSettings->Audio is a project-wide setting.

Is it possible to access the DopplerFactor from within the application, so we can modify it in each scene individually? Otherwise, the doppler effect sounds very distorted in some scenes, and is barely noticeable in others.

The AudioSettings class doesn't expose it so I would say probably not that easily. AudioSource has doppler level, so you could do this each time a scene loads:

float someDoppler = 0.45f;
foreach(AudioSource source in Resources.FindObjectsOfTypeAll(typeof(AudioSource)))
{
    source.dopplerLevel = someDoppler;
}

I have a better idea: Change the scale factor of your meshes when you import them so they will be in meters afterwards :) might be a bit simpler for you.