Indeed, As a pirate I would certainly not spend weeks digging an elaborate treasure vault that would need a full crew. Putting all of my goods at one location wouldn't look like a good idea either. I would rather bury my treasure at different locations, and not too deep so that the job can be done quickly with the help of a couple of "expandable" guys. This has the extra advantage that retrieving it is easier, and may serve as a life insurance if I get caught and tortured (or at least buy time and give chances to escape or be rescued).
This also probably requires a map. Carving it in stone is probably the best (memory fades, paper burn), but here I would use caution again and would not write everything on a single stone.
Perhaps it is more apt to imagine yourself as a semi-autonomous band of pirates, rather than as an authoritarian individual.
Their design challenges were both to hide loot from outsiders and to make it difficult for any smaller group of band members to return to the scene without alerting most of the others. This elaborate arrangement could have been designed to buy time for the rest of the group to hear about excavations and return to claim their share.
From having only read the article, my theory is that the band had discovered a naturally occurring shaft part-filled with sea water. They somehow blocked the base of the shaft then drained it with lowered buckets. It is feasible that their skin-divers were able to work from air pockets in the cavern below. Also, that the divers may have discovered a swimable route to open water.
With an empty shaft, they now needed to shore up and back-fill several times to make looting from below difficult and dangerous. They'd have been concerned about one of their number draining all the back-fill and treasure into the cavern using gunpowder. Hence they built many layers, each of which would have been very risky to tunnel into, even for someone who knew the design. The depth of the earth layers, partial air gap and strength of shoring materials might have been calculated to be particularly unstable, when not supported from below.
Since the treasure was be recovered from the top, it is most likely that the pit had worked exactly as intended. The treasure was already long gone before anyone else noticed the pit. Its trappings were left in place and made generations of greedy people the poorer. The message stone, if it existed, was a wind-up. Its spirit suggests it was done at the time of recovery. Pleased as they were to find everything as they'd left it. This had cost almost no effort for a lasting glow of satisfaction.
The pit itself had not been tremendously difficult to make either. So there is no reason to believe it had ever hidden more than just ordinary wealth.
This theory is not flawless. Nevertheless, I believe it makes sense to consider design parameters around building an untrusted network.
This also probably requires a map. Carving it in stone is probably the best (memory fades, paper burn), but here I would use caution again and would not write everything on a single stone.