Makes sense for the game to contain the "extra bones" for weapons and such, they are pretty much just markers/gameobjects that indicate to the game where to attach or do things, creating and appending empties in Blender is easy enough for that on my opinion and also not complicated to do in Blender, but it is true it could be something more complex for someone that is not as experienced in stuff like this and I also agree that it could be a higher barry of entry, but with a guide I don't think that should be too much of an issue, iirc bundles can be compatible with a game even if built on different versions of Unity and even if it wasn't the case, downloading a specific version of Unity isn't really complicated at all, I think making stuff in Unity could also open the possibility to import other types of assets into the game as well in the future if you are looking into expanding the modding aspects of the game while mantaining it somewhat accessible while also making it easier for you to work on it on your end
Anyways, I love what you are doing and for what I am hearing that's an impressive work on the model importer, amazing job so far!!!, please take your time 🫡