### 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)

Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	ERR_FAIL_COND(!coords_level_proxies.has(from));
	coords_level_proxies.erase(from);
	emit_changed();
}
void TileSet::set_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from, int p_source_to, Vector2i p_coords_to, int p_alternative_to) {
	ERR_FAIL_COND(p_source_from == TileSet::INVALID_SOURCE || p_source_to == TileSet::INVALID_SOURCE);
	ERR_FAIL_COND(p_coords_from == TileSetSource::INVALID_ATLAS_COORDS || p_coords_to == TileSetSource::INVALID_ATLAS_COORDS);
	Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	from.push_back(p_alternative_from);
	Array to;
	to.push_back(p_source_to);
	to.push_back(p_coords_to);
	to.push_back(p_alternative_to);
	alternative_level_proxies[from] = to;
	emit_changed();
}
Array TileSet::get_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) {
	Array from;
	from.push_back(p_source_from);
	from.push_back(p_coords_from);
	from.push_back(p_alternative_from);
	ERR_FAIL_COND_V(!alternative_level_proxies.has(from), Array());
	return alternative_level_proxies[from];
}
bool TileSet::has_alternative_level_tile_proxy(int p_source_from, Vector2i p_coords_from, int p_alternative_from) {