### 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)

tile_lines_mesh.instantiate();
	tile_filled_mesh.instantiate();
}
TileSet::~TileSet() {
#ifndef DISABLE_DEPRECATED
	for (const KeyValue<int, CompatibilityTileData *> &E : compatibility_data) {
		memdelete(E.value);
	}
#endif 
	while (!source_ids.is_empty()) {
		remove_source(source_ids[0]);
	}
}
void TileSetSource::set_tile_set(const TileSet *p_tile_set) {