Godot Editor crashes when creating a pck file with a deleted .godot directory and adding fonts

### Tested versions

- Reproducible in: 4.3.stable

### System information

Ubuntu 22.04.5 LTS - Godot Editor 4.3.stable

### Issue description

If fonts are added to the project, and the **pck** file is created using **Godot Editor**, with the **".godot"** directory removed before that, then sometimes the **pck** file creation occurs with an error and Godot Editor crashes:
```reimport: begin: (Re)Importing Assets steps: 22
reimport: step 0: DejaVuSerifCondensed.ttf
reimport: step 10: DejaVuSansMono-BoldOblique.ttf
reimport: step 14: DejaVuSansCondensed-BoldOblique.ttf
ERROR: Caller thread can't call this function in this node (/root). Use call_deferred() or call_thread_group() instead.
at: propagate_notification (scene/main/node.cpp:2422)

=================================================================
handle_crash: Program crashed with signal 11
```

Example of a test project new-game-project, to reproduce:
[new-game-project.zip](https://github.com/user-attachments/files/17390277/new-game-project.zip)

Example of a script for playback:
[editor_loop_bug.zip](https://github.com/user-attachments/files/17390291/editor_loop_bug.zip)

The script input is the path to the Godot Editor executable file and the path to the new-game-project:
```
editor_loop_bug.sh -e -d
```

The script performs a loop deleting the ".godot" directory and creating a pck file:
```
for i in {0..100000}; do
clear
rm -rf $RESOURCE_DIR/.godot
${GODOT_EDITOR_BIN} --headless --path ${RESOURCE_DIR} --export-pack ${EXPORT_TEMPLATE} ${PCK_FILE}
if [[ $? -ne 0 ]]; then
echo "step failed"
exit 1
fi
done
```

### Steps to reproduce

1) Unpack the archive with the test project:
[new-game-project.zip](https://github.com/user-attachments/files/17390277/new-game-project.zip)
into a convenient directory

2) Run the editor_loop_bug.sh script:
[editor_loop_bug.zip](https://github.com/user-attachments/files/17390291/editor_loop_bug.zip)
specifying the path to the Godot Editor executable file and the path to the new-game-project as input:
```
editor_loop_bug.sh -e -d
```

3) Monitor the output

At the Nth iteration, Godot Editor will crash.

On my machine, sometimes the crash lasts for one minute, and sometimes 10 minutes or more

### Minimal reproduction project (MRP)

Example of a test project new-game-project, to reproduce:
[new-game-project.zip](https://github.com/user-attachments/files/17390277/new-game-project.zip)

Example of a script for playback:
[editor_loop_bug.zip](https://github.com/user-attachments/files/17390291/editor_loop_bug.zip)
The script input is the path to the Godot Editor executable file and the path to the new-game-project:
```
editor_loop_bug.sh -e -d
```

Start with the provided new-game-project.zip and editor_loop_bug.sh, running the headless --export-pack loop after deleting the .godot directory. Then inspect scene/main/node.cpp around propagate_notification at line 2422 and the reimport/export path. Done means repeated PCK creation with the added fonts completes without the thread error or an editor crash.

Written by the indexing model from the issue text.