For duty officers, as much as possible I try to use the color terms for the above reason.
For assignments, I do use the rarity, because for assignments color is basically yoked - when compared to other assignments of the same categorization - to rarity, and the expression of rarity communicates more useful information.
Color is a very useful UI element, but [due to existing convention], if we used a different color scheme people would be confused and frustrated, and where we use the conventional color scheme, people sometimes attach to it assumptions that are not always accurate in this context.
(Emphasis mine.) Therein lies the problem - pretty much every MMO has a fairly standard 'rarity' color scheme. At first, it usually works pretty well, as non-common items are only available as random drops with low percentages on the loot table, so that the stated rarity is pretty accurate. Then, the developers add new [end-game] rewards for dedicated players, and to make these items feel "special," they have to flag them as high-rarity items. Either one of two things happens then: 1) players soon find ways of easily farming these "ultra-rare" items, or 2) the devs want to be fair to all their players and make these items easy to acquire. Either way, they become extremely common, and thus, the rarity system is subverted.
I think the problem is exasperated by the fact that the rarity scheme may not necessarily work (or hasn't been designed accordingly - intuitively, that is) the way it was intended to work. It is causing confusion as you can see.
Ultra-rare Doffs should have their own color and/or some designation as such. Unique doffs as well (and/or both if they apply.)
e.g. A.) New color/naming convention for the ultra-rares. (as an alternative, a text description saying 'Ultra Rare' but with the same coloration would be fine) B.) Unique doff designation saying, "Unique" in clear text on the description of the duty officer.
The color has to be purple because purple indicates quality, and the quality is consistent.
That being said, some additional way of marking them as special is not a bad idea.