I saw no explanation of why my scenario gave a "flawed paradox legitimacy". So yes, if you don't mind.
The flaw as I see it would be that the speculations with the proposed givens in place (free will and omniscience) was your responsibility as an author to make sure it wasn't a false dilemma or that you could simulate a fabricated situation involving an omniscient God. A tall order to fill.
There are noticably other factors that are conveniently not addressed because of what appears as forced simplicity to what is allowed as a factor and it has thus far played out in a circular manner. While I read assertions that the prophetic outcome removes the choice, I don't see that as true.
The choice was still there.
There is the retort I've seen trying to claim a 'forced' choice, but that strikes me as much of a cop-out as I would with a criminal trying to put the burden of their choice on the shoulders of an authority holding them accountable.
For humor and if you wish to explore 'other possibilities', we could look at a legend of a prophet and an instance concerning two pigs for an example:
~~~
For instance, Nostradamus was a guest at the chateau de Fains when his host, the Seigneur de Florinville, had the chef bring out two pigs, a white one and a black one. The Seigneur de Florinville asked his famous guest Nostradamus to predict which pig they would be eating. Nostradamus predicted the black one. The host then secretly instructed the cook to serve the white pig. To prove the great psychic wrong the Seigneur de Florinville called the cook out during dinner and made him reveal which pig had been served. To the shock of the host the cook nervously replied "the black one" and explained that a wolf broke into the kitchen and had stolen the white pig as he was preparing it forcing the cook to serve the black one instead.
~~~
Not to give credence to the story, but the above could be used as an example of where the prediction was correct with the free will choice present.
The causality would be what explained how the two existed. In a similar manner, one could say box B was chosen, but for some causation -insanity, mistake, outside influences, rebellion, etc. - box A was the final outcome. Human behavior doesn't not always

follow the tidy collection of logical restrictions.
Your creation even avoids the option to pick both boxes or neither - again suspect of a false dilemma construction and simplification within a complex topic.
In reality? By all means, demonstrate the existance of choice in our universe. Indeed, demonstrate the existance of an omniscient in our universe.
Perhaps if I thought it would be of use or I was compelled for some reason, I might try despite the resistance I'm seeing with accepting the possibility of the two existing together. But I am not compelled.
But better yet, maybe we can all watch the Matrix twenty times and contemplate figuring out 'the why'. That factor in the topic seems to have more promise than hearing someone make grand claims about having proved something.
What do you mean by 'choice is separate from omniscience'? Do they exist at alternate times?
With the speculative nature of the topic, there could be the issue of time only being a factor for one and not restrictive for the other.
But I wasn't relying on that as a given.
I just don't see the presented argument 'proving' what it claims and allegedly succeeding where so many others have failed to 'prove'.
But if you insist that you've done it, let us know when you get published by a majority of authorities in the field. I could give a prediction on that, but admittedly I would be riding the probability factor in determinism.