I've found a workaround/solution to the color problem. Putting the SS3D effect on a non-transparent layer above the game layer followed by a Multiply effect will apply the colored lighting as expected to the game layer. However, if the Multiply effect is above SS3D in the effect order it will still do this to the final colors.
Viewing post in Update ss3light with tonemap comments
Thank you for taking some time on this, I've cleaned up the project pictured above for you to inspect. 😊
https://www.dropbox.com/s/6br77ep1ktlgtkg/FirstPersonLite01.c3p?dl=0