### 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)

occlusion_layers.clear();
	tile_lines_mesh.instantiate();
	tile_filled_mesh.instantiate();
	tile_meshes_dirty = true;
	
	physics_layers.clear();
	
	terrain_sets.clear();
	terrain_meshes.clear();
	terrain_peering_bits_meshes.clear();
	per_terrain_pattern_tiles.clear();
	terrains_cache_dirty = true;
	
	navigation_layers.clear();
	custom_data_layers.clear();
	custom_data_layers_by_name.clear();
	
	source_level_proxies.clear();