I still get the same message from the repeated lines, that the complex systems behind the surface can't be beautiful, and are somehow innately terrible.

In context, the poet's meditation on death sounds like an eastern philosophy thing, in which case the surface/depth discussion is about dualities. To say that one thing is beautiful implies that something else is not. The poet is asking his beloved whether he is accepted completely, or only his surface parts.

To put it another way, given the context, I interpret it as saying that the division between surface and depth is what makes one terrible and the other beautiful. Together, the whole is neither ugly nor beautiful. (Note the poet's meditation on his own depth and death does not indicate that he thinks they are bad things.)

But of course, that's just, like, my opinion, man. ;-)