### 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)
toolbar->add_child(button_advanced_menu);
	toolbar->add_child(memnew(VSeparator));
	button_pixel_snap = memnew(MenuButton);
	toolbar->add_child(button_pixel_snap);
	button_pixel_snap->set_flat(false);
	button_pixel_snap->set_theme_type_variation("FlatMenuButton");
	button_pixel_snap->set_tooltip_text(TTR("Toggle Grid Snap"));
	button_pixel_snap->get_popup()->add_item(TTR("Disable Snap"), SNAP_NONE);
	button_pixel_snap->get_popup()->add_item(TTR("Half-Pixel Snap"), SNAP_HALF_PIXEL);
	button_pixel_snap->get_popup()->add_item(TTR("Grid Snap"), SNAP_GRID);
	button_pixel_snap->get_popup()->connect("index_pressed", callable_mp(this, &GenericTilePolygonEditor::_set_snap_option));
	snap_subdivision = memnew(SpinBox);
	toolbar->add_child(snap_subdivision);
	snap_subdivision->get_line_edit()->add_theme_constant_override("minimum_character_width", 2);
	snap_subdivision->set_min(1);
	snap_subdivision->set_max(99);
	Control *root = memnew(Control);
	root->set_v_size_flags(Control::SIZE_EXPAND_FILL);
	root->set_custom_minimum_size(Size2(0, 200 * EDSCALE));
	root->set_mouse_filter(Control::MOUSE_FILTER_IGNORE);
	add_child(root);
	panel = memnew(Panel);
	panel->set_anchors_and_offsets_preset(Control::PRESET_FULL_RECT);
	panel->set_mouse_filter(Control::MOUSE_FILTER_IGNORE);
	root->add_child(panel);
	base_control = memnew(Control);
	base_control->set_texture_filter(CanvasItem::TEXTURE_FILTER_NEAREST);
	base_control->set_anchors_and_offsets_preset(Control::PRESET_FULL_RECT);
	base_control->connect("draw", callable_mp(this, &GenericTilePolygonEditor::_base_control_draw));
	base_control->connect("gui_input", callable_mp(this, &GenericTilePolygonEditor::_base_control_gui_input));