I've always liked the |\ and ~` caps to match the mods in colors. I'd love it if group buys would include those caps in both color schemes for those people who like symmetry (like me) and for those who prefer them to match the alphas. The cost difference would be marginal, but, IMO, it would look so much nicer.
On the topic of logic, there is no logic to it at all, not so far as I can see. If we only had the modifiers different colors, we'd have to make Tab, Backspace, and Enter the same color as the alphas, not just ~` and |\, as those keys are not modifier keys. I suppose I should add Caps Lock in there too since, technically, it's not a modifier key. The layout like that has, as far as I can tell, always been an aesthetic thing.