Instantiate Child Scene Keyboard Shortcut strange behavior on MacOS

### Tested versions

- Reproducible in 4.3.rc2, 4.3.dev5, 4.3dev4, 4.2.2.stable (and probably more, only tested these versions)

### System information

Godot v4.3.rc2 - macOS 14.6.0 - Vulkan (Forward+) - integrated Apple M2 Pro - Apple M2 Pro (10 Threads)

### Issue description

The default keyboard shortcut Shift+Command+A to instantiate a new child scene doesn't work at first. Upon clicking Shift+Command+A, "Godot" in the menu bar flashes, see attached video. When pressing the button with the mouse it opens as expected. But then, when clicking on "Godot", and hovering over "Services" and closing the menu again, the keyboard shortcut suddenly works. Just pressing on "Godot", but not hovering over "Services" does not make the shortcut work.

https://github.com/user-attachments/assets/84048862-e802-4aef-ba87-3d9655888fce

### Steps to reproduce

This works for me everytime I start a brand new project. Then I do what I described above and what is visible in the screen recording. I suspect that this is due to me updating to the newest MacOS version (Sonoma 14.6), because I don't think I experienced this before updating.

### Minimal reproduction project (MRP)

N/A

Start by reproducing the Shift+Command+A behavior in a brand new Godot project on macOS 14.6, using the tested Godot versions and the attached recording as reference. Trace the editor shortcut and macOS menu handling; done means the shortcut opens the child-scene dialog immediately without first interacting with the Godot or Services menus.

Written by the indexing model from the issue text.