As for the case being used with a transitive verb 見つける, で can indicate the location where the agent is at, not always the location of the object. For instance, in a sentence 人ごみの中で彼女を見つけた, the agent (= the speaker) and the object (= her) would be both in the crowd, whereas the speaker might not in the crowd in 人ごみの中から/に彼女を見つけた. The two locations would be the same place in most cases, though (as in your example 金貨を海の底で見つけた).