As far as OP's question - freeboard to me means from waterline to where the water would roll into the boat, ie how much hull exists above the waterline. Although as you load a boat up this changes some, mostly it's a matter of the sheer - how tall the hull is designed (ie 6 inches worth of weight is a shit ton of weight for a given boat, while one otherwise similar hull to another can easily be 6 inches +/- freeboard wise).
Cockpit depth is a different consideration where the deck height comes into play.
Then a self bailing deck adds a different set of considerations where you are balancing cockpit depth, and headroom, against height above the waterline, and you need pitch to assure the water actually rolls to the stern and leaves the boat (assuming your drains/scuppers are on the transom)..
On a skiff, keep in mind you really do not need a self bailing deck to begin with, bilge pumps can get the job done just fine and then you need not worry about all this stuff. It would need to be a stout boat under 20 feet for me to consider building it with a self bailing deck, ie lots of freeboard so the deck can be set adequately tall...
But with a boat on a trailer, the nice thing is you can easily enough put it in the water, see how it sits - use objects like concrete blocks or drums of water placed to approximate the weight of what you plan to add, and witness the waterline if you want.