### 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)

if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		if (p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES || p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_SIDES) {
			if (p_peering_bit == TileSet::CELL_NEIGHBOR_RIGHT_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_LEFT_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_TOP_SIDE) {
				return true;
			}
		}
		if (p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES || p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			if (p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_CORNER ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_CORNER ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_TOP_LEFT_CORNER ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_TOP_RIGHT_CORNER) {
				return true;
			}
		}
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		if (p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES || p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_SIDES) {
			if (p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE) {
				return true;
			}
		}
		if (p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES || p_terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			if (p_peering_bit == TileSet::CELL_NEIGHBOR_RIGHT_CORNER ||
					p_peering_bit == TileSet::CELL_NEIGHBOR_BOTTOM_CORNER ||