### Godot version

4.2 dev1

### System information

Windows 10.0.19045 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1060 (NVIDIA; 30.0.15.1403) - Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz (8 Threads)

### Issue description

Calling `Tree.propagate_check()` after an item is unchecked does not properly uncheck the parents. They are left in partially checked state.

It's easy to observe in theme editor:

https://github.com/godotengine/godot/assets/2223172/71d0479c-0a5e-48d3-957f-d90379a95c22



### Steps to reproduce

1. Edit a Theme resource
2. Go to Manage Items... menu
3. Go to Import Items tab
4. Unfold something
5. Check and uncheck a child checkbox

### Minimal reproduction project

N/A
ERR_FAIL_INDEX(p_column, cells.size());
	if (cells[p_column].custom_bg_color && cells[p_column].custom_bg_outline == p_bg_outline && cells[p_column].bg_color == p_color) {
		return;
	}
	cells.write[p_column].custom_bg_color = true;
	cells.write[p_column].custom_bg_outline = p_bg_outline;
	cells.write[p_column].bg_color = p_color;
	_changed_notify(p_column);
}
void TreeItem::clear_custom_bg_color(int p_column) {
	ERR_FAIL_INDEX(p_column, cells.size());
	cells.write[p_column].custom_bg_color = false;
	cells.write[p_column].bg_color = Color();
	_changed_notify(p_column);
}
Color TreeItem::get_custom_bg_color(int p_column) const {
	ERR_FAIL_INDEX_V(p_column, cells.size(), Color());
	if (!cells[p_column].custom_bg_color) {
		return Color();
	}
	return cells[p_column].bg_color;
}
void TreeItem::set_custom_as_button(int p_column, bool p_button) {
	ERR_FAIL_INDEX(p_column, cells.size());
	cells.write[p_column].custom_button = p_button;
	cells.write[p_column].cached_minimum_size_dirty = true;
}
bool TreeItem::is_custom_set_as_button(int p_column) const {