### 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)
int16_t x = decode_uint16(&local[0]);
		int16_t y = decode_uint16(&local[2]);
		if (p_format == TileMapLayer::FORMAT_3) {
			uint16_t source_id = decode_uint16(&local[4]);
			uint16_t atlas_coords_x = decode_uint16(&local[6]);
			uint16_t atlas_coords_y = decode_uint16(&local[8]);
			uint16_t alternative_tile = decode_uint16(&local[10]);
			set_cell(Vector2i(x, y), source_id, Vector2i(atlas_coords_x, atlas_coords_y), alternative_tile);
		} else {
#ifndef DISABLE_DEPRECATED
			
			uint32_t v = decode_uint32(&local[4]);
			
			bool flip_h = v & (1UL << 29);
			bool flip_v = v & (1UL << 30);
			bool transpose = v & (1UL << 31);
			v &= (1UL << 29) - 1;
			
			int16_t coord_x = 0;
			int16_t coord_y = 0;
			if (p_format == TileMapLayer::FORMAT_2) {
				coord_x = decode_uint16(&local[8]);
				coord_y = decode_uint16(&local[10]);
			}
			const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
			if (tile_set.is_valid()) {
				Array a = tile_set->compatibility_tilemap_map(v, Vector2i(coord_x, coord_y), flip_h, flip_v, transpose);
				if (a.size() == 3) {
					set_cell(Vector2i(x, y), a[0], a[1], a[2]);
				} else {