### 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)

if (terrain_set >= 0) {
						ERR_FAIL_INDEX_V(terrain_set, get_terrain_sets_count(), Vector<Vector<Ref<Texture2D>>>());
						LocalVector<int> bit_counts;
						bit_counts.resize(get_terrains_count(terrain_set));
						for (int terrain = 0; terrain < get_terrains_count(terrain_set); terrain++) {
							bit_counts[terrain] = 0;
						}
						if (tile_data->get_terrain() >= 0) {
							bit_counts[tile_data->get_terrain()] += 10;
						}
						for (int terrain_bit = 0; terrain_bit < TileSet::CELL_NEIGHBOR_MAX; terrain_bit++) {
							TileSet::CellNeighbor cell_neighbor = TileSet::CellNeighbor(terrain_bit);
							if (is_valid_terrain_peering_bit(terrain_set, cell_neighbor)) {
								int terrain = tile_data->get_terrain_peering_bit(cell_neighbor);
								if (terrain >= 0) {
									if (terrain >= (int)bit_counts.size()) {
										WARN_PRINT(vformat("Invalid terrain peering bit: %d", terrain));
									} else {
										bit_counts[terrain] += 1;
									}
								}
							}
						}
						for (int terrain = 0; terrain < get_terrains_count(terrain_set); terrain++) {
							if ((bit_counts[terrain] > counts[terrain_set][terrain].count) || (bit_counts[terrain] == counts[terrain_set][terrain].count && tile_data->get_probability() > counts[terrain_set][terrain].probability)) {
								counts[terrain_set][terrain].count = bit_counts[terrain];
								counts[terrain_set][terrain].probability = tile_data->get_probability();
								counts[terrain_set][terrain].texture = atlas_source->get_texture();
								counts[terrain_set][terrain].region = atlas_source->get_tile_texture_region(tile_id);
							}