Not sure KO can be done in either style because the large ships are troop carriers as well. The ships ,outside the gunhauler, are costed as troop carriers and their warscrolls are built around moving troops about. It is why they have always been lacking in armour and damage output. They would not work like other behemoth armies.
Actually thinking about it, you could have two warscrolls for each ship, including the gunhauler. One that allows troops to be carried , let's say 3 ballon boys for a gunhauler, 10 foot troops for the frigate and 15 for the ironclads plus the rule for more troops equals movement loss. Then the other warscrolls could be straight up battle ships with higher armour and better weapons but they lose the troop carrying ability.
For the non troop version you could have make different KO heros into the captain of each ship and have them unlock different abilities. An admiral as captain of a ship could unlock the abilitie to make ships battleline. Khemist could unlock double shoots on a ship etc.
Would require a complete rework but that's what new battletomes are for.