The way You presented here is not only tedious, it is also blocking any option of reimporting assets.
What You are looking for is post_import tool scripting. Create new script :
tool
extends EditorScenePostImport
func post_import(scene):
And than You can manipulate the root ( scene ) any way You want, but You have to return it. For example :
func post_import(scene):
scene.replace_by(yourcustombody)
return yourcustombody
Or manually rechild mesh instances to new custom body and so on, You will figure it out :)
Now You just place this script in Import Settings in custom script
slot and press reimport