The metaphysical conceits are the speaker's love as compared to the compass and the speaker's love compared to gold "to airy thinness beat"--it only spreads when beaten, but does not break.

The metaphors you speak of are unfamiliar to me, but looking back, the first stanza speaks of a man who dies--his chapter ends. Life is temporary, and so are chapters. The speaker says he passes quietly without worry about where he is going since he is a devout man, and that the speaker's parting from his love should be the same.  They know they love each other and that absence will not change this, so they should leave one another without "tempests" and profane crying.

The second metaphor you mention might be the speaker's reference to the universe and the uncertainty men suffer from when comets, earthquakes, and other natural phenomena occur. However, he mentions these things take place out in space and we don't worry about it since we don't know of it.  He also mentions that he is completed by his love and that no matter how far away from her he travels, like the compass legs that spread wide apart to create a large circle, he will return to the center, his center: her.  Perhaps this is the 'man as part of a continent' metaphor.  He is constant as a continent in his love for her.