I never really thought about why Dali depicted it like that, other than that it's more visually interesting than the standard view, or at least is so because it's so unconventional.
Also, I've always 'read' the image as Jesus floating in the sky over the water below.
"On the bottom of his studies for the painting, Dalí explained its inspiration: "In the first place, in 1950, I had a 'cosmic dream' in which I saw this image in colour and which in my dream represented the 'nucleus of the atom.' This nucleus later took on a metaphysical sense; I considered it 'the very unity of the universe,' the Christ!"
[2]"
"Although it is a depiction of the
crucifixion, it is devoid of nails, blood, and a crown of thorns, because, according to Dalí, he was convinced by a dream that these features would mar his depiction of Christ."