afterwardsis not a paint. I dries clear and you won't see it once it is dry, but it will bind the skull fragments to the bone and prevent further flaking. The skull may have a low shine to it afterwards, but the color will be natural. You can also use matte finish modge podge instead of the Elmer's glue. You can get that at the hobby stores. It is used to glue puzzles together.
The rain over the years leached out the calcium in the bone that's why its flaky. Boiling does the same thing to bone, just faster. In nature that's called chemical weathering.
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