Duplicating a node tree with a @tool script that edits global_position/global_rotation causes nodes to lose their transforms

Tested versions

• Reproducible in: v4.2.1.stable

System information

Godot v4.2.1.stable - Windows 10.0.22631 - Vulkan (Forward+) - dedicated NVIDIA GeForce RTX 3060 Laptop GPU (NVIDIA; 31.0.15.5176) - AMD Ryzen 5 5600H with Radeon Graphics (12 Threads)

Issue description

Duplicating a node tree with a @tool script that edits global_position/global_rotation causes nodes to lose their transforms.
A spam of scene/3d/node_3d.cpp:343 - Condition "!is_inside_tree()" is true. Returning: Transform3D() errors print in the console.

https://github.com/godotengine/godot/assets/39361911/9985cc7f-d814-413c-a53a-0601109b8230

Steps to reproduce

Create a Node3D, with a set of Node3D children
Attach a @tool script to the children that has a function that changes global_position/global_rotation
Create a exported bool "button" that allows the function to be called from the inspector, such as @export var function: bool = false : set = function_exec
Duplicate the Node3D

Minimal reproduction project (MRP)

Script_Position_Bug.zip

Start with the linked Script_Position_Bug.zip reproduction and follow the reported errors at scene/3d/node_3d.cpp:343 during Node3D duplication. Reproduce the @tool script that changes global_position/global_rotation, then verify that duplicating the tree preserves node transforms without the is_inside_tree() errors.