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After a little research, I think I've figured it out, maybe. The object is either a unique groyne marker (the path leading to the object certainly resembles a groyne) or it might be an ornamental reference to the Satamisaki lighthouse in Minamiosumi, in Kagoshima Prefecture. Lilycove is geographically closer to the real-life Kanoya (also in Kagoshima Prefecture), but this object we see in the game - later turned into a lighthouse - is at the very tip of Hoenn's mainland geography. Similarly, the Satamisaki lighthouse exists at the extreme southern point of Japan's mainland geography. Moreover, the shape of the lighthouse more closely resembles the object in-game, though this changes in ORAS, where it looks like the Slateport lighthouse instead.
