My conclusion is that Confusion in Line can move the Master Spy to a different position in line without him moving back. This conclusion is based on the principal that consistency of rules trumps authorial intent. The explanation follows.
As noted in this question, there is an official answer from Wizards of the Coast here:
An Action Card is played - the Action Card is carried out - the Master
Spy is moved to the back of the line
There is no way to play a card to get the master spy to the front of the line without him just going back
after the cards effects.
The Master Spy has the ability:
After each action card is played, move this card to the end of the line.
What this put together seems to imply is that the resolution of an action card is included in the playing it, and the Master Spy moves only after the card has finished it's resolution and has been placed face up in the play area or in the discard. Then, the Master Spy will move regardless of whether or not the card had an effect (so playing Fountain of Blood which is just worth two points but doesn't do anything will still cause the Master Spy to move).
Now we are left with two options in the case of Confusion in Line:
Option 1: Take the WotC's answer to the letter.
This means that we pay particular attention to their point that there is no way whatsoever possible in the who wide game to manipulate the line such that the Master Spy does not end up at the end. And there is your answer. You play Confusion in Line, and then the Master Spy ends up at the end.
This is an unsatisfactory answer because it isn't well reasoned. It's saying the Master Spy's ability trumps Confusion in Line's ability because... it just does. Author's intent is irrelevant without an official FAQ or card specific ruling. This is not how I play Guillotine. For that, move on to option 2.
Option 2: Use what we know about other WotC products (namely Magic the Gathering) to create a consistent rules framework for Guillotine.
There are three phases to a turn in Guillotine:
Play an action card (optional)
Collect the first noble in line
Draw an action card
Confusion in Line creates a delayed triggered ability that takes affect in phase 2 of the turn of the player of your choice. It must be in phase two, because if it were during phase 1, a player could avoid the trigger by not playing an action card on their turn (in which case Confusion in Line would read "Randomly rearrange the line after that player plays an action card".
With this framework, we can also determine that the Master Spy moves to the end of the line at the end of phase 1. Thus, phase 1 (if the player chooses to have it) has the following steps:
Play action card
Put action card on table or in discard as appropriate
Move Master Spy (if relevant)
Repeat these steps if you are allowed to play another action card
Let's say you chose yourself with Confusion in Line. The resolution of effects for Confusion in Line is merely the creation of the delayed trigger. It is then discarded. The Master Spy so cleverly moves to the end. Then we move on to phase 2. The line gets shuffled. The Master Spy is at the front! You scoop him up and get a delicious four points.
Then, on the next player's turn, they play an action card and the Master Spy leaves your score area to go back to the end of the line :P (just kidding; although this might not be a joke since apparently "Clerical Error... end[s] the day and discard[s] all nobles in line if used to get Robespierre from someone else's score pile."; noble abilities working from score areas is a whole other rats nest that we will kick elsewhere).
Anyways, I like this option flavor-wise as well because it means even the Master Spy is thrown off by mass confusion (there is no good information for him to act off of).