Most definitely a very oddball serial prefix — not just for a 5906 of that vintage, but it’s just not a typical serial prefix that S&W has used for anything mainstream.
I believe your theory about it being a run for a specific LE contract makes the most sense.
Other ideas that seem reasonable (if unlikely….?) is that it was a replacement frame made later than the pistol originally shipped. But this idea doesn’t make sense considering the box end label looks period-correct down to the wear and coloring on it.
The 6-digit product code has the leading “6” which is proper S&W-speak for “used gun” as it notes on the end label but it makes sense to mention exactly what constitutes a used gun in S&W factory speak.
It doesn’t mean that Billy Bob bought it at Gun ‘R Us and stuck it under the seat of his F-150. Rather it means that the factory took it back in to inventory and it could have been a contract over run, it could have been factory serviced from a large contract, it could have been a saleman’s sample gun, it could have spent time at a SHOT Show or similar industry or trade show, perhaps fondled by many or even used for live fire in some promotional event for the brand.
Oh man…
I have a friend that has a really crazy rare 1-of-1 S&W pistol and according to the box label, it too was a used gun. It was shipped to Jerry Miculek and eventually returned “to inventory.” I don’t know how he got it.

It’s awesome. But it’s just another crazy example of what gets coded by the factory as a used gun.
Oh, actually I have one also, although it is a revolver. It appears as new in box and even shows evidence of the factory test fire and no other use… but wears the leading 6 product code and a secondary box end label over the original as a used gun. It’s a mint 16-4.
I would certainly send an e-mail to S&W with that serial number and 6-digit product code and see what kind of reply you get.
But — I would bet a crisp newone dollar bill that if you asked S&W once and then again at a later date… or if you e-mailed and then later called on the phone… you may very well get two different answers. And you would get a better answer with a factory letter, but that’s a $100 exercise, may be hard to justify.