### 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)
PackedStringArray features = PackedStringArray(p_project_features);
	PackedStringArray supported_features = _get_supported_features();
	for (int i = p_project_features.size() - 1; i > -1; i--) {
		if (!supported_features.has(p_project_features[i])) {
			features.remove_at(i);
		}
	}
	
	PackedStringArray required_features = get_required_features();
	for (int i = 0; i < required_features.size(); i++) {
		if (!features.has(required_features[i])) {
			features.append(required_features[i]);
		}
	}
	features.sort();
	return features;
}
#endif 
String ProjectSettings::localize_path(const String &p_path) const {