Jobs have very iconic appearances, and it just makes sense to me that SE wants to preserve those very iconic appearances in the armor they create specifically for those jobs. You can most definitely place the Maelstrom emblem on your gear, but I wouldn't expect Square to allow much more than that.
As for the other sets of gear... Yeah, I guess I could agree that it would be nice to dye the other dungeon sets, even if I think their appearance is perfectly fine as is. In a way, I suppose it could be kinda like the "artifact" gear for the crafting and gathering classes: looks great without dyeing, but looks okay if you dye it anyway.