### 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)
Pair<StringName, StringName> feature_override(feature, p_name);
					if (!feature_overrides.has(s[0])) {
						feature_overrides[s[0]] = LocalVector<Pair<StringName, StringName>>();
					}
					feature_overrides[s[0]].push_back(feature_override);
				}
			}
		}
		if (props.has(p_name)) {
			props[p_name].variant = p_value;
		} else {
			props[p_name] = VariantContainer(p_value, last_order++);
		}
		if (p_name.operator String().begins_with("autoload/")) {
			String node_name = p_name.operator String().split("/")[1];
			AutoloadInfo autoload;
			autoload.name = node_name;
			String path = p_value;
			if (path.begins_with("*")) {
				autoload.is_singleton = true;
				autoload.path = path.substr(1);
			} else {
				autoload.path = path;
			}
			add_autoload(autoload);
		}
	}
	return true;
}
bool ProjectSettings::_get(const StringName &p_name, Variant &r_ret) const {