Well, I think there's a big difference in how a faction icon looks, and how it is presented in the space that is reserved for it. I'm all for very different and distinct faction icons, with all kinds of shapes and colors.
Thing is, it's not quite clear if we are seeing rectangular flags here, or symbols with a background. In the former case, it's all well, the factions make their flags as they like and the UI just shows them. (Then most of them would surprisingly similar, though.) But in the latter case, if these are symbols on some filler background (and that's how I understood it), the UI has to arrange them on that background anyway. So why would it not do that in a unified way?