### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
}
void TileDataDefaultEditor::_notification(int p_what) {
	switch (p_what) {
		case NOTIFICATION_ENTER_TREE:
		case NOTIFICATION_THEME_CHANGED: {
			picker_button->set_icon(get_editor_theme_icon(SNAME("ColorPick")));
			tile_bool_checked = get_editor_theme_icon(SNAME("TileChecked"));
			tile_bool_unchecked = get_editor_theme_icon(SNAME("TileUnchecked"));
		} break;
	}
}
Variant::Type TileDataDefaultEditor::get_property_type() {
	return property_type;
}
TileDataDefaultEditor::TileDataDefaultEditor() {
	label = memnew(Label);
	label->set_text(TTR("Painting:"));
	label->set_theme_type_variation("HeaderSmall");
	add_child(label);
	picker_button = memnew(Button);
	picker_button->set_theme_type_variation("FlatButton");
	picker_button->set_toggle_mode(true);
	picker_button->set_shortcut(ED_SHORTCUT("tiles_editor/picker", TTR("Picker"), Key::P));
	toolbar->add_child(picker_button);
}
TileDataDefaultEditor::~TileDataDefaultEditor() {
	toolbar->queue_free();
	memdelete(dummy_object);
}
void TileDataTextureOriginEditor::draw_over_tile(CanvasItem *p_canvas_item, Transform2D p_transform, TileMapCell p_cell, bool p_selected) {