### 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)

csd.autotile_coords = d[key];
					} else if (key == "one_way") {
						csd.one_way = d[key];
					} else if (key == "one_way_margin") {
						csd.one_way_margin = d[key];
					} else if (key == "shape") {
						csd.shape = d[key];
					} else if (key == "shape_transform") {
						csd.transform = d[key];
					}
				}
				ctd->shapes.push_back(csd);
			}
		} else if (what == "occluder") {
			ctd->occluder = p_value;
		} else if (what == "navigation") {
			ctd->navigation = p_value;
			/*
		// IGNORED FOR NOW, they seem duplicated data compared to the shapes array
		} else if (what == "shape") {
		} else if (what == "shape_offset") {
		} else if (what == "shape_transform") {
		} else if (what == "shape_one_way") {
		} else if (what == "shape_one_way_margin") {
		}
		// IGNORED FOR NOW, maybe useless ?
		else if (what == "occluder_offset") {
			// Not
		} else if (what == "navigation_offset") {
		}