I would cut the hole in the hull, and then saturate the open wood grain and let that set up for a day and then put the skeg box in with a filet on the inside. You can even wrap some light weight cloth around the hull opening into the skeg box.

You could even give that saturation coat a second pass and let that set up before installing the box if you want to be really sure. You want to install the box as soon as the epoxy hardens to the touch so you get a chemical bond with the filet on the inside box to hull connection.