### 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)

ERR_FAIL_COND_MSG(!tiles.has(p_atlas_coords), vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	ERR_FAIL_INDEX(p_frame_index, (int)tiles[p_atlas_coords].animation_frames_durations.size());
	ERR_FAIL_COND(p_duration <= 0.0);
	tiles[p_atlas_coords].animation_frames_durations[p_frame_index] = p_duration;
	emit_signal(SNAME("changed"));
}
real_t TileSetAtlasSource::get_tile_animation_frame_duration(const Vector2i p_atlas_coords, int p_frame_index) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), 1, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	ERR_FAIL_INDEX_V(p_frame_index, (int)tiles[p_atlas_coords].animation_frames_durations.size(), 0.0);
	return tiles[p_atlas_coords].animation_frames_durations[p_frame_index];
}
real_t TileSetAtlasSource::get_tile_animation_total_duration(const Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), 1, vformat("TileSetAtlasSource has no tile at %s.", Vector2i(p_atlas_coords)));
	real_t sum = 0.0;
	for (const real_t &duration : tiles[p_atlas_coords].animation_frames_durations) {
		sum += duration;
	}
	return sum;
}
Vector2i TileSetAtlasSource::get_tile_size_in_atlas(Vector2i p_atlas_coords) const {
	ERR_FAIL_COND_V_MSG(!tiles.has(p_atlas_coords), Vector2i(-1, -1), vformat("TileSetAtlasSource has no tile at %s.", String(p_atlas_coords)));
	return tiles[p_atlas_coords].size_in_atlas;
}
int TileSetAtlasSource::get_tiles_count() const {
	return tiles_ids.size();
}
Vector2i TileSetAtlasSource::get_tile_id(int p_index) const {