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.