User blog comment:Diego Brando/Phantom Blood (Doubt about coffin)/@comment-5919632-20131203033250/@comment-1739368-20141127024804

This seems to be the most reasonable answer. People seem to overlook it, but the manga also specifically stated that the coffin they pulled out of the ocean was empty but had a secret compartment underneath it. Kinda funny how the most non-canon light novel did its research.