### 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 texture;
}
void TileSetAtlasSource::set_margins(Vector2i p_margins) {
	if (p_margins.x < 0 || p_margins.y < 0) {
		WARN_PRINT("Atlas source margins should be positive.");
		margins = Vector2i(MAX(0, p_margins.x), MAX(0, p_margins.y));
	} else {
		margins = p_margins;
	}
	_clear_tiles_outside_texture();
	_queue_update_padded_texture();
	emit_changed();
}
Vector2i TileSetAtlasSource::get_margins() const {
	return margins;
}
void TileSetAtlasSource::set_separation(Vector2i p_separation) {
	if (p_separation.x < 0 || p_separation.y < 0) {
		WARN_PRINT("Atlas source separation should be positive.");
		separation = Vector2i(MAX(0, p_separation.x), MAX(0, p_separation.y));
	} else {
		separation = p_separation;
	}
	_clear_tiles_outside_texture();
	_queue_update_padded_texture();
	emit_changed();
}
Vector2i TileSetAtlasSource::get_separation() const {