Now we can start to see the issue in Linear mode (you may need to click the image to enlarge it). The color lerp for the fog is no longer matched perfectly to the background skybox (notice the hard line at the horizon). Nothing else has changed from the previous screenshot other than the color mode. You can see problems with the sun shafts and lens flare as well; however, those are less of an issue because they can be tuned appropriately to compensate. The fog color lerp cannot be compensated. The start and end colors of the lerp are correct (see the Dawn example), but the colors in between are incorrect.

This simple problem caused us a huge headache. The beginning and ending points of our time-of-day transitions still matched the skybox perfectly, but every point in between was too dark and made our horizon line stick out like a sore thumb. So what was going on in Linear mode that was different from Gamma mode?

We had no idea. After scouring the web I came up empty handed. So I ended up resorting to posting for help on the /r/Unity3D subreddit. Lo and behold we were presented with a potential solution in less than an afternoon. And surprisingly, the solution came from real-world light physics and not from a Unity-specific error. As it turns out, Linear mode in Unity does not properly calculate the blending of two colors, but we can do that ourselves if we apply math! The video below led us to our final equation.