Being anxious to figure this out I pm'd Oleg from zmodeler and he said (if I understand him right) that zmodeler basically doesn't touch collisions on wdr files.
I tried importing a shipping container into zmodeler, that I can spawn anywhere and have it be solid. I then turned around and exported it from zmodeler without any changes. I can still spawn it anywhere and have it be solid. So that makes me think there are two types of collision files in gta iv. Some hard coded based on map location, and some that are coded to match spawnable object locations.
Can anyone confirm or deny that theory? If so I'd be very interested in learning more about the second type.
Thanks for any help.