Sunset and evening star, And one clear call for me! (1-2)
In the same way that the sun "goes home" for the night, so, too, must the speaker. He's being called, and it is hard not to think of that call as a summons to return home to meet his maker, who is, in this case, God.
When that which drew from out the boundless deep Turns again home! (7-8)
It seems like the speaker is talking about his soul, which will "turn again home" after he dies. It's almost as if the life he is about to conclude wasn't "real," only a vacation or temporary separation from his true home.
Twilight and evening bell, And after that the dark! (9-10)
"Evening bell" recalls the second line of the poem, where the speaker talks about being called. In both lines, the speaker acts as though he is being summoned home or called back to the place he really belongs—the afterlife, which in this case is symbolized by the open ocean.
I hope to see my Pilot face to face When I have crossed the bar. (15-16)
The speaker hopes to meet his "Pilot," the guy that has guided and directed his whole life. It's a reunion of sorts, a homecoming.