I wouldn't say there's any "functionality" difference, I'm sure most of us don't rely very much on color-coded keys to find what to press.
I think the aesthetics can work either way. On my WASDv2 87 I currently have the Deep Space set with purple modifiers, `, and \ because I think it looks best. On my Das Pro4 I left the ` and \ the same color as my alphas. IMO as long as it's consistent (` and \ match), it looks good.