A scene file is loaded as a
PackedSceneclass instance, which inrehits
Resource class. When a scene is instanced, any child nodes will be instanced together.
You need to remove any node from an autoload scene if you don't want them to be instanced upon game starting.
Too achieve what you want, you can save all your bullet node as scene files. And use
var bullet_scene :PackedScene = preload("res://bullet01.tscn")
var bullet :Node = bullet_scene.instance()
bullet.rotation_degrees = rot
to instantiate a bullet node.
At this point, your BulletFactory becomes an empty scene. So maybe just remove
BulletFactory.tscn from AutoLoad and delete the scene file. Then add
BulletFactory.gd to AutoLoad, and give it a same name as the previous scene.
A gdscript (which has to inherits Node or its subclass) as an autoload, is the same as a scene as an autoload. Just without those predefined nodes.