Yes, AF refers to the class limited quest reward gear from FFXI.
While I agree with some of your points - SE does indeed have a history of assigning elemental strengths/weaknesses with colors - I do not see where this makes much sense in appearance of the crafted gear we wear.
We have materia to add stats to gear, and the materia can be color coded. Spell effects can be color coded as well so it is clear that a sword is slashing away with ice magic laced on the blade or a mage has just thrown a thunder spell because the bolt has purple sparkles shooting out of it - all that would be just fine with me.
When I look at players in my party or running past me through town, I don't look at their gear and think "oh that Lalafell is wearing a red outfit - must be a Gladiator!" I do notice if the gear is made of metal, cloth or leather. I know that if a player is wearing a coatee set, that player is most likely set to a crafting class - and the tool equipped lets me know at a glance which craft. The gear sets already let me know at a glance which class the player is likely on, the color should have remained the player's style preference.
For unique class restricted gear sets (such as something similar to FFXI's Artifact Armor) that signify a particular uniform, then I don't mind certain colors. Typically in uniforms, all of the pieces have already been designed to look nicely together anyway. When AF was worn in FFXI, it meant that player had done a hard quest chain, had attained a certain number of levels and was now a "Red Mage" or a "Warrior" etc. For Grand Company gear or other similar gear sets, color is again applied to indicate the allegiance to the chosen company - and again, the gear is designed to match when worn as a set. I am fine with this concept.
However, for crafted gear that several jobs can use, I don't want every color to indicate what stats are on the gear. The result is a confusing mixture of colors that don't all blend together well. It also removes individuality. Why does every player who wants certain stats have to wear the exact same matching color gloves? I don't like the decision to extend color to stats in crafted gear for multiple class pieces. This is especially true for sets where we can't dye all pieces of the set the same color.
Part of the dev response was that color could not be applied to every item - I am OK with that if it needs to be that way. However, I still don't see why a crafted glove in one color vs another should have different stats. I love that we can first make a plain uncolored version of a piece of gear and then apply color to it later - that part is what we asked for. Changing the stats and restricting which classes can wear the item merely by dying the item a new color was not.