It comes down to your preferred gameplay activities. I agree that they probably shouldn't be common. I'd personally put them in the uncommon category. If you actively search them out, the majority are fairly reasonable to get over time. The account wide achievements has helped this a bit as well. Trophies that drop from mobs that are typically only seen one at a time become a bit of a chore. Wamasu is one of the big ones that can cause a bottleneck.

I think you may find that while you personally feel these are the hardest dyes to get others may very well find the Grand Overlord dye exceptionally grindy to get as they may not play PvP as a preferred gameplay activity. At least in that situation, it's not categorized as common.

I had all the monster trophy dyes sometime in 2014 and I think I'll finally get my first Grand Overload during the next Mayhem event. That's just how my gameplay loop works out.