### 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)

terrain_meshes[terrain_mode] = mesh;
			}
			
			for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
				CellNeighbor bit = CellNeighbor(i);
				if (is_valid_terrain_peering_bit_for_mode(terrain_mode, bit)) {
					if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
						if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
							polygon = _get_square_corner_or_side_terrain_peering_bit_polygon(tile_size, bit);
						} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
							polygon = _get_square_corner_terrain_peering_bit_polygon(tile_size, bit);
						} else { 
							polygon = _get_square_side_terrain_peering_bit_polygon(tile_size, bit);
						}
					} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
						if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
							polygon = _get_isometric_corner_or_side_terrain_peering_bit_polygon(tile_size, bit);
						} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
							polygon = _get_isometric_corner_terrain_peering_bit_polygon(tile_size, bit);
						} else { 
							polygon = _get_isometric_side_terrain_peering_bit_polygon(tile_size, bit);
						}
					} else {
						float overlap = 0.0;
						switch (tile_shape) {
							case TileSet::TILE_SHAPE_HEXAGON:
								overlap = 0.25;
								break;
							case TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE:
								overlap = 0.0;