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Yes, the tank lid is the same construction.

The top is thin gelcoat with non-skid, followed by resin, cloth, 2 or 3 layers of plywood followed by cloth and resin.

Is the soft spot where you stand at the helm or very close to an inspection port?

Take some photos and post.

You should closely inspect all the hoses: Fuel fill, vent and supply. IF they don't say "alcohol resistant" along the sides, you should replace them while deck is up. Not hard.