I would absolutely love to get involved with the data mining of the ROM for this game, but alas I need to stick with Lufia for the time being (I have a lot of work left to do there)... But I am interested to see how treasure chests / items in treasure chests work...
Don't worry, I've got that covered. For Mystic Quest, how chests work is that in the sprite data, there is a specific byte that determines which index the sprite gets it's data from. If it's 03 or some other bitwise combination, then it's a scripted event. If it's 0B, then it's an enemy encounter. If it's 13, then it's a chest. How it works is that there is a chest index at $8000 that covers many different chests. Even though most chests in the game are refillable, they are all given a unique chest ID. Only values 00 to 1C are flagged(thus only that many chests can contain unique items), and the first byte in the sprite data matches that flag, or another event flag to hide the event if you trigger it and come back.
As for the Chest data in Lufia, each map has a script index that contains things like the chest data and other sprite data. However, it matches up to the level data which means that you could shift the contents of a chest, but you cannot relocate it without altering the map, and the map data is compressed(so is Mystic Quest but chests are relocatable).
The only thing is that I found where the auto events are located(seperate table), but can't find the co-ordinates or map designation data. This is important because without it, bosses can't be relocated since some of them(especially crystal bosses) are auto events.