As you say, why would Gaeta know about #3 and hope for her to wake? Be willing to die for it? Hard enough to understand why he would know about the final cylon. Why would #3 be “asleep in the shirt of man?” I admit I am not sure why the word shirt is used here. To me it either means dressed as a male, or simply among humanity.

BTW there has also been suggestion that it’s about the hybrid, who just woke and jumped the cylon base ship. Gaeta opens his eyes like he knows about it. Not sure how to explain this — perhaps the Hybrid is able to project something into Gaeta’s mind, and the rest of the song is just Hybrid induced muttering.

The song is too cryptic to not have a hidden meaning, though.