### Godot version

v4.0.2.stable.official [7a0977ce2]

### System information

Windows 10

### Issue description

The settings found in **application/config/project_settings_override** end up being written to the `res://project.godot` every time the editor is started.

I find this inconvenient, `res://project.godot` is always on the changelist in git because of this.

I think it would be better if settings with the same value as found in **application/config/project_settings_override** were persisted in `res://project.godot` **only** when set by the "editor interface" or "by code" and not by the "merge" that happens at the start of the editor.

### Steps to reproduce

1. Before opening the MRP in the editor, note **window/size/mode** value within `res://project.godot`;
2. Now open it in the editor and check the `res://project.godot`, notice that **window/size/mode** was changed by the contents of `res://project_override.cfg` (which is the **application/config/project_settings_override** file).

### Minimal reproduction project

[Projects Override Merging Into Project Godot.zip](https://github.com/godotengine/godot/files/11555239/Projects.Override.Merging.Into.Project.Godot.zip)
resource_path = current_dir;
		resource_path = resource_path.replace("\\", "/"); 
		err = _load_settings_text_or_binary(current_dir.path_join("project.godot"), current_dir.path_join("project.binary"));
		if (err == OK && !p_ignore_override) {
			
			_load_settings_text(current_dir.path_join("override.cfg"));
			found = true;
			break;
		}
		if (p_upwards) {
			
			d->change_dir("..");
			if (d->get_current_dir() == current_dir) {
				break; 
			}
			current_dir = d->get_current_dir();
		} else {
			break;
		}
	}
	if (!found) {
		return err;
	}
	if (resource_path.length() && resource_path[resource_path.length() - 1] == '/') {
		resource_path = resource_path.substr(0, resource_path.length() - 1); 
	}
	return OK;
}
Error ProjectSettings::setup(const String &p_path, const String &p_main_pack, bool p_upwards, bool p_ignore_override) {