If the sea represents death, well then sailing represents that long, slow journey toward death. Setting out from the safe harbor of life and into the great unknown of death is the central metaphor of "Crossing the Bar," and while it may seem obvious, it's definitely worth a closer look.
Line 4: The speaker is putting out to sea in this line, but given all we know about the poem, we know that this means he's heading out on his final journey—toward death.
Lines 5-8: Wanting the tide to clear the way for him, the speaker hopes for easy conditions, so he can get out of the harbor—or life—without too much ado.
Line 12: "Embark" here has, as you've probably realized by now, little to do with actually setting sail. It's a metaphor for leaving the land of the living and heading off for the afterlife.
Line 14: The flood, or sea, is bearing him toward death. And once he crosses the bar, there's no turning back.
Line 15: The "Pilot" here refers to God. It's the perfect culmination of the sailing-as-dying metaphor, since, as the pilot of the speaker's boat, God has been steering him on this course the whole time.