Trial of the Crusader's items appear to be faction specific still.
Example item: 47808
--Item is a alliance specific mace, unable to be equipped by Horde
-Steps to replicate:
--Create horde level 80
--.additem 47808
--Attempt to equip
Error received is: "You can never use that item"
When the item drops in a raid, the faction that cannot equip the item will not see the loot roll chance either. The items dropping (alliance \ horde) appear to depend on who starts the fight via the NPC in the arena, this may aid in testing.
I believe there may be a faction flag in the items_template database preventing it?
Please let me know if I can post more \ help research.