Using left click while having multiple viewports open and freelook mode active causes focus issue

### Tested versions

- Reproducible in 4.6.1.rc1, 4.6.stable, 4.5.1.stable, 4.5.stable, 4.4.1.stable, 4.3.beta1

### System information

Godot v4.6.stable - Windows 11 (build 26100) - Multi-window, 1 monitor - Direct3D 12 (Forward+) - dedicated NVIDIA GeForce RTX 3060 Laptop GPU (NVIDIA; 32.0.15.7260) - 12th Gen Intel(R) Core(TM) i7-12700H (20 threads) - 15.79 GiB memory

### Issue description

While in the editor if you have at least 2 viewports open, enter freelook mode in one of them and press left click, nothing out of the ordinary will appear to have happened as you can keep using it normally, but if you notice one of the other opened viewport, the one that has the center of the screen inside it, it has the highlight indicating that it currently has focus. After having pressed left click, if you exit freelook mode by using the right click button nothing erroneous happens, but if instead you attempt to exit by using shift + f you will activate freelook mode in a different viewport, causing both to be active at the same time, pressing shift + f again will cause you to exit the second freelook mode and your mouse will now be at the center of the screen.

Note:
- In versions 4.4.1.stable to 4.3.beta1 the issue can be reproduced although these versions have other issues related to the simultaneous use of freelook and viewports (#88670) that can make the issue harder to notice
- In version 4.2.1.stable the same behaviour can be observed although here it happens instantly with no need to left click

### Steps to reproduce

- Open a new project and go to the 3d workspace
- Select one of the viewport options in the view tab
- Toggle freelook mode on a viewport that doesn´t include the middle of the screen
- Press left click and shift + f
- Attempt to move mouse

### Minimal reproduction project (MRP)

N/A