### Godot version

3.5.2.stable, 4.0.1.stable

### System information

Arch Linux

### Issue description

When the `Show Hidden Files` property is enabled in the Editor Settings:
![image](https://user-images.githubusercontent.com/6501975/226908540-8e70e520-3dcd-46e4-beaf-103ac176c1de.png)
Any `FileDialog` nodes from the project will inherit this setting, and their `Show Hidden Files` property is set to true everytime the scene is re-opened:

https://user-images.githubusercontent.com/6501975/226909135-a8fafdf7-ca36-40aa-b69a-a7baf2d7ae4f.mp4


This occurs on 3.5.2 as well.

### Steps to reproduce

- Enable `Show Hidden Files` property in the Editor Settings:
    - Reload Godot for the bug to occur
- Create a FileDialog node, and set it's `Show Hidden Files` property to false
- Save and close the scene, and reopen it
- The `Show Hidden Files` property is reset to true.

### Minimal reproduction project

N/A
EditorProgress save("save", TTR("Saving Scene"), 4);
	if (editor_data.get_edited_scene_root() != nullptr) {
		save.step(TTR("Analyzing"), 0);
		int c2d = 0;
		int c3d = 0;
		_find_node_types(editor_data.get_edited_scene_root(), c2d, c3d);
		save.step(TTR("Creating Thumbnail"), 1);
		
		Ref<Image> img;
		
		
		
		if (c3d == 0 && c2d == 0) {
			img.instantiate();
			img->initialize_data(1, 1, false, Image::FORMAT_RGB8);
		} else if (c3d < c2d) {
			Ref<ViewportTexture> viewport_texture = scene_root->get_texture();
			if (viewport_texture->get_width() > 0 && viewport_texture->get_height() > 0) {
				img = viewport_texture->get_image();