The |\ key (and the ~` key) is not a modifier; it is an alpha. That's why it is colored like an alpha. This organizing principle is based on key purpose/functionality, not on an OCD-driven need for color symmetry. I prefer not to let the crazies dictate how we organize our keycaps, tyvm.
Besides, once you graduate to keyboards with more than 60 keys, color symmetry goes right out the window anyway, with the nav cluster weighing down the entire right side with mod-colored keys, and the numpad layout only half-surrounding the numbers (and period) with mod-colored operation keys (plus num lock and Enter). And then there's the alternating color blocks of F-keys, which makes no sense either functionality-wise or color-symmetry-wise. Best to just realize that the standard color/layout scheme we have is based on an ill-conceived IBM design and learn to embrace it since it's not going away any time soon.
As you said that colour symmetry goes out the window anyway, so why not throw it harder and use mod pipe lol.
Actually though, I did used to use `~ key in the modifier colour on the hhkb/tsangan layout because that keeps it all the colours the same, idk I've always found it looking weird that the beige hhkbs (the blanks especially) have the alpha coloured `~ key in the top right, maybes that's influenced by the fact that I had no idea why the keys were coloured differently until recently where I realised the obvious lol.
Also yeah why does the f-row alternate like that, that doesn't make sense but I think the IBM layout, was made to be useable to basically everyone and had everything there, even if it's not even the best layout that IBM did (the at is a lot better imo), so I guess some liberties were placed on making it look more aesthetically pleasing. I have a feeling this is true because they used to do full mod colour f rows on some of earliest examples of the modern layout with the ibm 3161 terminal, which is interesting to note.