### 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)
base_control->draw_texture(handle, xform.xform(polygon[j]) - handle->get_size() / 2, poly_modulate);
			}
		}
	}
	
	if (tinted_polygon_index >= 0) {
		Ref<Font> font = get_theme_font(SNAME("font"), SNAME("Label"));
		int font_size = get_theme_font_size(SNAME("font_size"), SNAME("Label"));
		String text = multiple_polygon_mode ? vformat("%d:%d", tinted_polygon_index, tinted_point_index) : vformat("%d", tinted_point_index);
		Size2 text_size = font->get_string_size(text, HORIZONTAL_ALIGNMENT_LEFT, -1, font_size);
		base_control->draw_string(font, xform.xform(polygons[tinted_polygon_index][tinted_point_index]) - text_size * 0.5, text, HORIZONTAL_ALIGNMENT_LEFT, -1, font_size, Color(1.0, 1.0, 1.0, 0.5));
	}
	if (drag_type == DRAG_TYPE_CREATE_POINT) {
		base_control->draw_texture(handle, xform.xform(in_creation_point) - handle->get_size() / 2, Color(0.5, 1, 2));
	}
	
	if (hovered_segment_index >= 0) {
		base_control->draw_texture(add_handle, xform.xform(hovered_segment_point) - add_handle->get_size() / 2);
	}
	
	base_control->draw_set_transform_matrix(xform);
	tile_set->draw_tile_shape(base_control, tile_xform, grid_color, false);
	base_control->draw_set_transform_matrix(Transform2D());
}
void GenericTilePolygonEditor::_center_view() {
	panning = Vector2();
	base_control->queue_redraw();
	button_center_view->set_disabled(true);
}
void GenericTilePolygonEditor::_zoom_changed() {