### 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)

Vector<Vector2> point_list = {
		Vector2(3, (3.0 * (1.0 - p_overlap * 2.0)) / 2.0),
		Vector2(3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(2, 3.0 * (1.0 - (p_overlap * 2.0) * 2.0 / 3.0)),
		Vector2(1, 3.0 - p_overlap * 2.0),
		Vector2(0, 3),
		Vector2(-1, 3.0 - p_overlap * 2.0),
		Vector2(-2, 3.0 * (1.0 - (p_overlap * 2.0) * 2.0 / 3.0)),
		Vector2(-3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-3, (3.0 * (1.0 - p_overlap * 2.0)) / 2.0),
		Vector2(-3, -(3.0 * (1.0 - p_overlap * 2.0)) / 2.0),
		Vector2(-3, -3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-2, -3.0 * (1.0 - (p_overlap * 2.0) * 2.0 / 3.0)),
		Vector2(-1, -(3.0 - p_overlap * 2.0)),