### 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
bool ret_changed = false;
	List<PropertyInfo> pi;
	obj->get_property_list(&pi);
	for (const PropertyInfo &E : pi) {
		if (!(E.usage & PROPERTY_USAGE_STORAGE)) {
			continue;
		}
		switch (E.type) {
			case Variant::OBJECT: {
				Ref<Resource> res = obj->get(E.name);
				if (_find_and_save_resource(res, processed, flags)) {
					ret_changed = true;
				}
			} break;