Option Popup not visible under certain project settings

### Tested versions

Reproducible in 4.3-rc2 and 4.2.2

### System information

Godot v4.3.rc2 - Windows 10.0.19045 - Vulkan (Forward+) - dedicated AMD Radeon RX 6600 XT (Advanced Micro Devices, Inc.; 31.0.24026.1002) - Intel(R) Core(TM) i5-6600K CPU @ 3.50GHz (4 Threads)

### Issue description

The Popup of the Option button did not show up / is rendered off screen.

### Steps to reproduce

First set these display settings in project settings:
`window/size/always_on_top=true`
`window/subwindows/embed_subwindows=false`

Then create a scene with a OptionButton, set items in it. Now run the scene, and the Popup does not show up after clicking the Option Button. In 4.3 the Popup gets a position of 4000px+ on my device also (offscreen). Seems like the Popup should be rendered also always on top.

-> If you set `window/size/always_on_top=false` the Popup shows up as expected.

### Minimal reproduction project (MRP)

[Option-Click-Bug-4.3-rc2.zip](https://github.com/user-attachments/files/16479819/Option-Click-Bug-4.3-rc2.zip)
[Option-Click-Bug-4.2.zip](https://github.com/user-attachments/files/16479946/Option-Click-Bug-4.2.zip)