I agree that the new deck order ending of Emerge Triumphant is anti-climatic, but I disagree with your assumption that they can conclude that "the deck was never shuffled." First of, a false shuffle is meant to look like a real shuffle, and it DOES. If that isn't the case, perhaps in a regular triumph, a spectator could assume you never actually shuffled the cards face up and face down. Following your logic, a spectator would come to the conclusion that you gave them a different card when it changes in their hand, or that you switch it before you put it in the middle in an ACR.
The original triumph was performed with a push through shuffle (or strip out if you ask Johnny Thompson...), as the story goes, Vernon was able to do it so well that people thought it was a genuine shuffle. I don't doubt that a technique if done well, can fool and nullify the possibility that deception has occurred. However, this doesn't address the structuring issue of the effect. Following my logic, let's take the d0uble lift equivalent of what I believe to be a glaring structural flaw. You do a double to show three of clubs, you then apparently give this card to the spectator where it changes into the nine of diamonds, all is right in the world. However, what happens if you then show the spectator that the top card on the deck is the three of clubs? It gives them a foothold in which to work backwards. Since real magic obviously does not exist, the only logical explanation is that you switched the card as it gave it to them. I'm not saying that the effect won't fly this way, but it makes it easier for the spectator who is not in a moment of suspended disbelief to logically deduce the method. Good routines are structured to block out potential methods of backtracking. Vernon's Ambitious Card routine published in Stars of Magic is a good example of this principle.
I used to perform Emerge Triumphant and never got caught. While the end does detract from the standard triumph climax, it is in no way "structurally flawed." Whether or not a piece of an effect is relevant to the other is arguable - for example effects where a deck just changes color for no apparent reason. The instant download, "Revolver," comes to mind. What matters is the reactions - it doesn't matter what the magician thinks about the trick.
The age old argument. I used to perform a very sloppy side steal, but I've never gotten caught either, that doesn't mean that it wasn't a bad side steal. What we're ultimately looking to achieve is art right? Because we can get away with sloppy technique and bad routining does not mean that it is a good justification. As for if an effect is relevant or not, that depends on the way you choose to present your work. Fitzkee gives the now classic example. If you were in the middle of a conversation, and you produce a ham sandwich out of the air, people might be amused, but no body cares. However, if someone mentioned that they were hungry, and you reach out and produce a sandwich, now the effect has context, it has proper framing and now there's a reason for someone to care, to relate. Watch Tommy Wonder perform, he exemplifies the roles drama and theatre should play in a performance. What matters is reactions, but an artist must care about his craft and he must work to perfect it, otherwise he cannot achieve greatness in his art.