### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

return terrain_set;
}
void TileData::set_terrain(int p_terrain) {
	ERR_FAIL_COND(terrain_set < 0);
	ERR_FAIL_COND(p_terrain < -1);
	if (tile_set) {
		ERR_FAIL_COND(p_terrain >= tile_set->get_terrains_count(terrain_set));
	}
	terrain = p_terrain;
	emit_signal(SNAME("changed"));
}
int TileData::get_terrain() const {
	return terrain;
}
void TileData::set_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit, int p_terrain_index) {
	ERR_FAIL_INDEX(p_peering_bit, TileSet::CellNeighbor::CELL_NEIGHBOR_MAX);
	ERR_FAIL_COND(terrain_set < 0);
	ERR_FAIL_COND(p_terrain_index < -1);
	if (tile_set) {
		ERR_FAIL_COND(p_terrain_index >= tile_set->get_terrains_count(terrain_set));
		ERR_FAIL_COND(!is_valid_terrain_peering_bit(p_peering_bit));
	}
	terrain_peering_bits[p_peering_bit] = p_terrain_index;
	emit_signal(SNAME("changed"));
}
int TileData::get_terrain_peering_bit(TileSet::CellNeighbor p_peering_bit) const {