the climbing animations for ladders are seperate from the ladders. What i mean by that is if you changed the distance of the ladder rungs the animations would not be affected and look very odd. The units however are not seperate from the ladders. One way to look at the ladders is a strip of land that requires a different animation to walk across it. The ladders in seige towers work the same way. The platforms within the seige towers are needed (the units actually stand on them). Also Im pretty sure that you cant change around the inside of seige towers as i believe the path the units take is hardcoded. Removing or changing the ladders and/or platforms may disrupt this path and cause the units not to be able to walk up the tower.

As for units starting with seige equipment im almost positive this is impossible but i cant say that for certain. I know you can get a unit to have a seige engine but i doubt if it could be used correctly.