Or, the layers of timbers are trees felled in the same 100y storms, etc.

The flooding tunnel is likely just a normal geological feature, not some super-clever drift tunneling technique.

The stone is likely a fraud. Who would place a cryptic sign 90 feet down, telling themselves (in secret writing) to keep digging? Wouldn't they presumably know that they hadn't reached their treasure yet? Wouldn't they be more likely to place an innocuous sign on the surface, such as a gravestone? It's more likely a way to con investors out of further funds.

It's probably nothing but a rumor.