[4.6 RC2] When debugging a game, Godot leaves some space

### Tested versions

- Tested in 4.6 RC2
- Not any other version

### System information

Godot v4.6.rc2 - Zorin OS 18 on Wayland - X11 display driver, Multi-window, 1 monitor - Vulkan (Forward+) - integrated Intel(R) HD Graphics 5500 (BDW GT2) - Intel(R) Core(TM) i3-5005U CPU @ 2.00GHz (4 threads) - 7.67 GiB memory

### Issue description

This happened to me 5 mins ago:

Once in a while, while debugging a game, these side spaces are left unused.
After restarting the game:

### Steps to reproduce

Is hard to reproduce, happens once in a while

### Minimal reproduction project (MRP)

N/A

No source files, tests, entry points, or minimal reproduction project are provided. Start by reproducing debug launches on Godot 4.6 RC2 with Wayland and the X11 display driver, comparing the initial window with a restarted game; done means the side spaces no longer appear intermittently.

Written by the indexing model from the issue text.