The deck on a Hobie 17 is foam cored - but this is overkill. You're taking what should be a 1/2 hr job and turning it into an all day project.

Seal the edges of the foam with polyester resin. Doesn't have to be pretty, since it'll be hidden by the port mounting flange.

You don't need to use the mounting screws. Use a good silicone product (3M Marine Grade Silicone Sealant), run a bead around the inside corner of the mounting flange and set it in the hole.

Even if you use the "contoured" ports, the curvature of the deck is greater than the curvature cut into the flange. You'll have a gap that varies from 0 at the centerline of the hull to about 3/16 at the edge of the flange. Just level it and let cure overnight (if you want - you can proceed immediately to the next step if you're careful not to move the port).

Come back the next day and shoot more silicone around the edge of the mounting flange, filling up the space under the flange (it'll squirt out the mounting screw holes). Use a wet finger to smooth out the fillet around the mounting flange and the screw holes. Let cure overnight again and you're done.

BTW, always mount an inspection port with the lid in place. Keeps the flange from warping.