I don't see why we have to think that both of those need to be following the same color schemes.
We could easily have 2 different schemes for the junk loot and the trophies.
And thinking about it, the junk loot doesn't even need tiered by color anyway. They could all look the same and it wouldn't change anything. You go to the junk dealer, open a trade, click the junk button, it all trades away for coin...
The trophies, having them colored makes sense, since you need trophies of the correct tier to do turn-ins for EXP.
A better use of the artists' time who is working on all of these, would be splitting the 5 tiers of trophies into 20 or 21 tiers. So that each 5-Level range of trophies has its' own color, plus a color for level 100 (Tier 6). This would be an actual useful change.
Keep the current colors, then split each tiers' color into 4 versions that slightly vary it. Perhaps a dimmer to brighter scaling. This would be immediately obvious and intuitive which tier a trophy is part of.
The proposed change just feels like we are changing for no useful reason.
And as far as learning the colors, and the fact that they are different than "other mmo's colors" is not a big deal in the slightest. A level 1 player isn't going to be looting a t5 trophy and go "omg!, I have no idea what this color means?!?!" You learn the colors as you level and loot them... And you don't get both junky gear (gray) plain gear (green) and elite gear (purple or orange) from whatever mob you are hunting. Our armor and weapons are primarily all crafted. It's a totally different system, and makes no sense to try and copy the colors used in a completely different loot system.
So my vote would be:
Junk loot: Don't care in the slightest
Trophies: Split into unique colors for every 5 level range, plus a color for t6. And each group of 4 5 level ranges that line up with the tiers, keep them similar enough that we can tell the trophies tier (Since the tier determines the cities where they can be turned in).
The proposed changes feel like we they are being changed for no reason other than to just change them... (it's pointless)