Node duplication issue with @tool

### Tested versions

4.2, 4.3 stable

### System information

Godot v4.3.stable - Windows 10.0.19045 - GLES3 (Compatibility) - Radeon RX 560 Series (Advanced Micro Devices, Inc.; 31.0.14001.45012) - Intel(R) Core(TM) i5-4570 CPU @ 3.20GHz (4 Threads)

### Issue description

I noticed a strange problem when duplicating nodes in the scene tree that were added by a plugin, I first encountered this problem in [my plugin](https://github.com/JekSun97/gdTree3D/issues/1) developed using GDExtension, now I decided to test this problem locally in the editor itself using GDScript plugins, and this problem repeated.

If we duplicate a node added using GDExtension or a plugin and `@tool`, then the node is duplicated twice, the more we duplicate this node, the more descendants it has

When reloading a project, extra nodes are sometimes shown in the editor, sometimes not, which is also quite strange.

### Steps to reproduce

1. Open MRP
2. Create a new node added by the "newnode" plugin
3. Duplicate it
4. You will see extra descendants in the output window

### Minimal reproduction project (MRP)

[bugdublicate.zip](https://github.com/user-attachments/files/17654469/bugdublicate.zip)

Start by opening the attached bugdublicate.zip minimal reproduction project in Godot 4.3 and follow the listed steps: create the node from the newnode plugin, duplicate it, and inspect the output and scene tree. The issue is done when plugin or GDExtension nodes using @tool duplicate only once and reloading the project does not produce extra descendants.

Written by the indexing model from the issue text.