Using different methods to implement non-embedded child windows will trigger the always_on_top breaks non-embedded popups problem

### Tested versions

4.3 Until now

### System information

Windows 10 x64

### Issue description

We can get non-embedded child windows in the following two ways:
- disabling embed_subwindows.
- Change `force_native` of a subwindow

When using the second method, it seems that the parent window of the subwindow is not handled correctly. This causes all pop-ups on the subwindow to use the main window as its parent window(This is a guess). This further causes the position of the pop-ups of the subwindow to be wrong, and after `always_on_top` is enabled on the subwindow, it will cause the window sorting to be wrong and cover all the pop-ups of the subwindow.

### Steps to reproduce

- Create default project
- Add `Window` node, enable `always_on_top` and `force_native`, disable `visible`
- Add any node with popup menu (e.g. TextEdit) to window node
- Run
- Make the window node visible
- Open the popup menu on window node

*The PopopMenu is not only covered but also displayed in the wrong position.*

### Minimal reproduction project (MRP)

[issue_100192_mrp.zip](https://github.com/user-attachments/files/18059912/issue_100192_mrp.zip)

Start with the attached issue_100192_mrp.zip project on Windows 10 and reproduce the popup behavior using a Window with force_native and always_on_top. Investigate the Window and PopupMenu handling for non-embedded child windows and compare it with the embed_subwindows path. Done means the subwindow popup is correctly positioned and remains above the subwindow without being covered.

Written by the indexing model from the issue text.