As the article mentions, the most dangerous aspect of the landing may have been the turbulence and downwash over the fantail. Given that this was a STOL airplane (and also given that the pilot would have had no experience landing on a target moving at almost his stall speed) it might have been safer if the ship just pointed its flight deck into the wind.
I recall from flight school one instructor who liked to demonstrate that the aging Cessna 150 he was often assigned to could be landed in the width of a runway (as performed at an intersection.)
it might have been safer if the ship just pointed its flight deck into the wind
Reading TFA, that's precisely what occurred:
Chambers ordered his chief engineer to transfer the ship’s electric load to the emergency diesel engines and make steam for 25 knots (29 mph)... The captain turned his ship into the wind to prepare for a fixed-wing landing.... Buang lowered the Bird Dog’s flaps and approached in a shallow descent at a speed of 60 knots (69 mph). With the ship providing an estimated 40 knots (46 mph) of headwind to aid the landing, the light plane slowly caught up.
15 knot headwind plus ship's speed gave 40 kt landing wind, aircraft landed at stall speed of 60 kt airspeed, giving 20 kt to kill on landing. That was a risk on a slick deck, and from the accompanying video the landing was fairly far down the deck, but had sufficient braking distance.
I mean just pointing its flight deck into the wind with sufficient speed to hold it there, as opposed to heading into it at 25 knots (which required firing up six boilers, so I assume it was not initially steaming at that speed.)
It was always possible that the airplane could have gone off the bow with insufficient speed to do a go-around, but it might also be the case that the shallow approach was a consequence of trying to land on a target moving away, and that made it difficult to spot-land. My guess is the latter, though of course I can't prove it.
With a 40 kt wind down the deck, one would need the brakes to avoid being blown backwards off it, or into a reverse groundloop which might well lead to the same outcome.
Even just holding position would give some downdraft, from those 15 kt of wind. With 2/3 of airspeed compensated by the ship moving into the wind, and an airplane already quite good at short runway landing, the descent angle relative to the moving runway should easily be steep enough to stay clear of the downdraft.
Yet the pilot apparently made a shallow approach. I suspect that was due to having not landed on a moving target before - setting up the approach for where the ship was, not where it was going to be when he got there.
At first sight, it might seem the situation is just like a high-wind landing on an airfield, but there is a difference: on an airfield, if you line up for, say, a 3-degree approach, but the wind is stronger than you anticipated, you will need more power, it will take longer, and your descent rate will be reduced, but your flightpath will be as planned, with that 3-degree slope. In the case of a ship moving away from you, not only will you need more power than anticipated, but the path you follow will be shallower than planned, as it ends further away than anticipated.
Pilot not only had no experience on carrier landings, but no comms as to how to approach.
There were two practice approaches, so the mobile-landing element may not have been as significant as you're suggesting. That's of course hard to say either way.
An alternative view on the two practice approaches (or go-arounds?) is that he still made a shallow approach over the fantail.
The lack of communications means that the pilot could not be warned of the specific difficulties and dangers of landing on a moving aircraft carrier, over and above the ordinary difficulties of a short-field landing of the sort every pilot is supposed to be proficient in. In that circumstance, my guess is that minimizing the novel dangers would be the way to go, but, as you say, we are all just guessing here.
I recall from flight school one instructor who liked to demonstrate that the aging Cessna 150 he was often assigned to could be landed in the width of a runway (as performed at an intersection.)