This underwater structure clips into the Pelion Rift, and two chests are completely unobtainable due to this. The only way I could fully explore this structure is by waiting for the accessible chests to respawn.
(Proof that the chests are inside the rift, using Revealing Potion)
If you pick up the chests after they start respawning, the notification on exploration you get will tell you that you have n amount of chests remaining, and that number is always correct (shows how many chests are there in that exact moment), but picking up respawned chests still counts towards exploration.
In other words, every single chest you open at the structure will always contribute to the exploration, but the in-game notification will always show the true amount of chests at the structure at that moment