### 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)
bool in_top_right_triangle = (in_tile_pos - Vector2(0.5, 0.0)).cross(Vector2(0.5, 1.0 / overlapping_ratio - 1)) > 0;
			switch (tile_layout) {
				case TileSet::TILE_LAYOUT_STACKED:
					ret = ret.floor();
					if (in_top_left_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? 0 : -1, -1);
					} else if (in_top_right_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? 1 : 0, -1);
					}
					break;
				case TileSet::TILE_LAYOUT_STACKED_OFFSET:
					ret = ret.floor();
					if (in_top_left_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? -1 : 0, -1);
					} else if (in_top_right_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? 0 : 1, -1);
					}
					break;
				case TileSet::TILE_LAYOUT_STAIRS_RIGHT:
					ret = Vector2(ret.x - ret.y / 2, ret.y).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(0, -1);
					} else if (in_top_right_triangle) {
						ret += Vector2i(1, -1);
					}
					break;
				case TileSet::TILE_LAYOUT_STAIRS_DOWN:
					ret = Vector2(ret.x * 2, ret.y / 2 - ret.x).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, 0);