Reading this over, if I'm understanding correctly, you want to be able to load a custom mesh (the sword in your example) and have it automatically move to stay on/in the hand of your character model, even through animations.
Try adding a Spatial node as a child of your arm model (if it is a separate mesh from the base of your character model) and place it near the hand. Add a child MeshInstance and set its mesh as the mesh of the item being held when needed. The Spatial should be affected by the rotation of its parent.
In the event you have a single mesh character model, you can still use the Spatial node idea, but you will have to set up a separate animation that will play and affect the Spatial node. Again, set a MeshInstance as the child of this Spatial node and have its mesh attribute set to whatever item is being held.
I recommend this based on the little knowledge I have of 3D animation in Godot and the testing I tried.