Would boats fight underwater? Whole new concept of naval combat.
I think you should skip ships until the engine allows surface fighting in the seas.
It sounds a fun idea for a mod. With a world full of huge trampling monsters I can easily see humans fielding smaller, more portable, machines to battle them. Scorpion ballistas, smaller catapults or even oil cannons spewing flames (For T'ien Ch'i atleast). Just stay clear of regular siege engines as they would be useless in a battlefield. As far as I can tell the "Siege" command takes the construction and use of siege engines into mind. How else would they be storming fortresses?