The thunderhead is clearly a metaphor for violence and war, destructive offshoots of the dream-ideal. The element of theft is hinted at too ("pirate-ship"), so this might be a reference to Nostromo. The sea itself will also be a symbol in the novel, standing for freedom, so the image of the flaming thunderhead "engaging the sea" translates to violence and theft, born of illusion, opposing freedom. "Engaging," however, also means "marrying" (again hinting at a Nostromo reference), suggesting a more complex and interdependent relationship between violence and freedom.