scene.useLogarithmicDepth cannot affect the result of scene.enableDepthRenderer. Logarithmic depth values should be exported as expected

[Evgeni_Popov]

See my answer in this thread:

ShaderMaterial and Logarithmic Depth Buffer

Starting from 5.0 you can use your own material to render a mesh with the depth renderer. So, simply call depthRenderer.setMaterialForRendering(yourMesh, yourMesh.material) and you should be good. You could also optimize things by providing a specific material instead of the true one of the mesh, where only the logarithmic depth is enabled, because the depth renderer is only interested in generating a depth value - the color value computed by the fragment shader is not used.