### 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)
if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.y /= overlapping_ratio;
	} else { 
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.x /= overlapping_ratio;
	}
	
	if (tile_shape == TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE || tile_shape == TileSet::TILE_SHAPE_HEXAGON || tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		
		
		if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			
			Vector2 raw_pos = ret;
			if (Math::posmod(Math::floor(ret.y), 2) ^ (tile_layout == TileSet::TILE_LAYOUT_STACKED_OFFSET)) {
				ret = Vector2(Math::floor(ret.x + 0.5) - 0.5, Math::floor(ret.y));
			} else {
				ret = ret.floor();
			}
			
			Vector2 in_tile_pos = raw_pos - ret;
			bool in_top_left_triangle = (in_tile_pos - Vector2(0.5, 0.0)).cross(Vector2(-0.5, 1.0 / overlapping_ratio - 1)) <= 0;