Thanks, guys. Turns out when I looked carefully at the bottom of the deck, it was not as recessed as I expected. There is a slight recess, but the skylight is almost a solid hunk. I could drill through it, but it would not be as nice is some others I have done.
On the other hand, I am not drilling out and glazing the portholes on this build anyway, so I guess covered skylights would be appropriate.