I put sealant between the C-box and the roof and used stainless fasteners and then added sealant inside the box as well. Every box I have seen is not fully waterproof when mounted horizontally, even the box from AMsolar.
With my setup I could see that there was 1/2" thick particle board before I made the hole for the cables. I avoideded any kind of gland or nipple as it would have interfered with routing the cables inside the cabinet that was below the box. I did use waterproof glands with the 10-2 cables from the panels.