If the only thing you changed is the weapons stats in the prototype definition, you can do that without copying the entire mod. Add Aircraft to your dependency list, then all you need is your data.lua to modify the values that the Aircraft mod already put in in data.raw.car["gunship",] etc.
Then you won't have to worry about conflicts or integrating changes when the original mod updates.
I appreciate the suggestion, I'll have to look into doing that. Really, I made this mod just for my friends and a server we're running, just wanted it to be easily available online for everyone to download. But if there's any widespread interest in it I can try and figure out how to do as you've suggested, I've just never made any other mods for Factorio before hence this really dirty version.