From patch 1.2, any orange (custom) appearance in the game will be viable for endgame purposes. Of course there'll be new outfits as well - so these changes together should lead to a very significant amount of variation in endgame, for all classes.
Just to clarify: are you simply restating that mods in end game set gear can be taken out and put into orange gear?
If so, what about the gear's set bonuses? Are there plans to put the set bonuses on the mods instead of the armor pieces themselves so we can port the bonuses over to orange gear?
If not, I'm not sure how viable orange gear will be for end game even with removable mods from end game gear.