I've been experimenting with the siege engine plug in from dfhack and am enjoying tossing landmines and captured invaders at incoming sieges. I've also been using cheap stone cages and throwing invaders into my volcano. I have noticed that with a catapult the custom ammo like blocks, cages, etc won't fire through fortifications. I tested to make sure it wasn't just the blocks not showing the flying animation and launched a few landmines and they opened inside of the fortification. When the fortifications were removed and I used a lowering bridge instead everything flew fine. Standard stones would still fire through the fortifications.
Just thought I'd mention it. Maybe someone has found a work around. But if not it'd be quite a bit of !Fun! if you tried throwing some giant captured goblin mount at another type of invader only to have the cage burst open one tile away from your legendary siege operator.
Of course my set up had the catapult right up against the fortification, if that matters. I'm not sure but maybe the custom ammo is spawning in the center of the catapult so it's not counting as being able to pass through the fortification.