" It just seems like the spoke holder, even if not used, is of very little consequence, so I don't know why it bothers some people."
It bothers me because it has become emblematic of a touring bike, and I think it is a bad design. So it is symbolic in my mind. As you say, what is the harm. If it were + or - some number of bottle mounts or other, I would not have the same issue. But it might be more serious. So yeah, it's a little silly to care. I certainly don't expect others to feel the same way I do. But as a very occasional builder, I think long and hard about frame design, and it sorta irks me when a few recognizable, superficial features are all of a sudden the difference between a serious touring design and another. It should be 25 on the list of features, but it is more often say 5.
Here is my test. I'm 52, and I remember when equally good bikes to the LHT didn't have hardly any BOs. Back then racks, shifters, bottle mounts, etc... on hard core commercial bikes were clamped on. Lots of BOs was mostly a custom thing. So here is my poser vs non-poser test for a BO. Would you clamp one on? If your otherwise fabulous frame came without rack mounts, or light mounts people would P-clip/clamp them on. I have yet to ever see that done with spokes. I am not talking about taping them on the frame, or zip tying them. Where is the clamp on fitting? In fact a clamp-on might even be better since it would be very adjustable and could even be moved left right if required. I think it is largely a cosmetic thing so it thrills when it is OEM but otherwise there is no clamor.