"Mysteries are not necessarily miracles," said Goethe. And that is about as succinct a statement as you might make of the difference between a religious naturalist and a supernaturalist.
Consider what is surely the most spectacular scientific discovery of the past century, maybe ever: the constructional machinery of life. Four chemical bases on a spiral helix -- A, C, G and T. A always pairs with T, C always pairs with G. The unique order of the base pairs determines the organism. Each triplet along the sequence (ACT, GAA, etc.) codes for one of twenty molecules called amino acids. A sequence of linked amino acids (typically hundreds long) is a protein. Proteins do all the work of an organism -- carrying oxygen, building tissue, breaking down food. ( I paraphrase Sean Carroll.) It is stunning in its elegance and simplicity.
There are 64 different triplets of A, C, G and T, but only 20 amino acids. A good computer programmer might have found a way to use all the possible combinations. In fact, there is some repetition; some different triplets code for the same amino acid, and three triplets act as "punctuation," like a capital letter at the beginning of a sentence and a period at the end. But still, how all this came to be is fraught with mystery. Jaw-dropping, heart-stopping mystery.
But mysteries are not miracles. Mysteries are puzzles to be illuminated. Every puzzle solved leads deeper into mystery. And the deepest of all mysteries, where all interrogations end -- unnamed, subsuming all our ignorance, glimpsed as through a glass darkly -- is the ground of the religious naturalist's faith, which is to rigorously pursue knowledge wherever it leads us, and in the end, faced with the limits of our knowing, to humbly say "yes" to the world.