The F-row is separate from the main cluster, and they're literally function keys, not alphanumerics. So breaking them up both spacing-wise and visually makes sense, since having a line of 12 very similar looking keys in a row would lead to the user searching for the right key, which would be less efficient.
In the main cluster mods being one color, and the alphanumerics being another makes sense.
If you want a mod colored tilde or pipe key just for visual symmetry that's fine, but it breaks the convention of why those keys are colored the way they are.