@tool script node is part of a sub-scene in another context, Error message during copying

### Tested versions

4.3-stable ~ 4.4-beta3

### System information

Godot v4.4.beta (5da6deaac) - Windows 10 - Multi-window

### Issue description

This isn't a bug, but the message might be unnecessary.

This error message was not displayed prior to version 4.3.
Consider moving this message to the notification area, as opposed to the output or debugger.


### Steps to reproduce

n/a

### Minimal reproduction project (MRP)

[test_proj.zip](https://github.com/user-attachments/files/18760038/test_proj.zip)

Start by opening the attached test project and reproducing the message on the listed Godot 4.3–4.4 versions. The issue does not name a file, test, or entry point; done would require deciding whether the message should be removed or moved from the output/debugger to the notification area.

Written by the indexing model from the issue text.