### 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)

#include "tile_set.h"
#include "core/core_string_names.h"
#include "core/io/marshalls.h"
#include "core/math/geometry_2d.h"
#include "core/templates/local_vector.h"
#include "core/templates/rb_set.h"
#include "scene/gui/control.h"
#include "scene/resources/convex_polygon_shape_2d.h"
#include "servers/navigation_server_2d.h"
void TileMapPattern::_set_tile_data(const Vector<int> &p_data) {