### Godot version

4.1.stable

### System information

Godot v4.1.stable - Windows 10.0.19045 - Vulkan (Compatibility) - Intel(R) HD Graphics 4600 (Intel Corporation; 20.19.15.5126) - Intel(R) Core(TM) i3-4330 CPU @ 3.50GHz (4 Threads)

### Issue description

When I try to join 68 images of 128x128 resolution in an atlas it returns a transparent 1x1 image

I tried using few images and it doesn't work either

It doesn't work either with 16x16, 32x32, 64x64 resolutions

- Google Translate :)

### Steps to reproduce


https://github.com/godotengine/godot/assets/136469511/ca5f64c2-f0c5-486f-a13e-b941ae2dea7d



### Minimal reproduction project

N/A
if (!tile_set_atlas_source) {
		return;
	}
	Ref<Texture2D> texture = tile_set_atlas_source->get_texture();
	if (texture.is_valid()) {
		Vector2i margins = tile_set_atlas_source->get_margins();
		Vector2i separation = tile_set_atlas_source->get_separation();
		Vector2i texture_region_size = tile_set_atlas_source->get_texture_region_size();
		Vector2i grid_size = tile_set_atlas_source->get_atlas_grid_size();
		EditorUndoRedoManager *undo_redo = EditorUndoRedoManager::get_singleton();
		undo_redo->create_action(TTR("Remove tiles in fully transparent texture regions"));
		List<PropertyInfo> list;
		tile_set_atlas_source->get_property_list(&list);
		HashMap<Vector2i, List<const PropertyInfo *>> per_tile = _group_properties_per_tiles(list, tile_set_atlas_source);
		for (int i = 0; i < tile_set_atlas_source->get_tiles_count(); i++) {
			Vector2i coords = tile_set_atlas_source->get_tile_id(i);
			Vector2i size_in_atlas = tile_set_atlas_source->get_tile_size_in_atlas(coords);
			
			if ((coords.x + size_in_atlas.x) > grid_size.x || (coords.y + size_in_atlas.y) > grid_size.y) {
				continue;
			}
			
			Rect2i region = Rect2i(margins + (coords * (texture_region_size + separation)), texture_region_size * size_in_atlas);
			bool is_opaque = false;