Yes, it plays with replacing entities. The thing is that two days ago I added support for all correctly coded vehicle mods. As helicopter mod doesn't use raise_script_built events not much can be done to add support for it.
When some mod creates any object (vehicle, turret or absolutely anything else) it must set special flag or run special method to let other mods know about it, except when creating some temporary service object or persistant controller object (player inside copter, autodrived vehicle, etc.). And helicopter up in the air is not a temporary object - it moves around, interacts with friendly and enemy objects. At least I hope so. I didn't play with this mod - don't know the idea... maybe flying copter should be invincible, do not collide automatically with anything, including acid streams from enemies spitters and worms or pvp rockets.
You can contact mod author about possibility to change it. Technically it's not a big problem to fix it - to add a flag in create_entity for main heli body and/or other objects creation, and better to add flag for destroy.
