Viewport Render is stretching when `window.borderless` is `true`

### Tested versions

4.2.2

### System information

Godot v4.2.2.stable - Windows 10.0.22621 - GLES3 (Compatibility)

### Issue description

- In borderless mode the viewport stretch toward the top and side (where the title bar was) and the mostly top of the viewport being cropped.
I take some screenshot via `get_viewport().get_texture()` and it fine.
- The mouse position doen't match the one display which again confirm the stretching

### Steps to reproduce

Put a visual element near the top of the game screen (control node)
Toggle borderless mode (via the inpector - remote scene `root` window/viewport)

The provided project:
- has both `Sprite2D` and `TextureRect`
- A button to toggle borderless mode
- Some (maybe usefull) Stats
- A `TextureButton` and mouse position marker

### Minimal reproduction project (MRP)

[Issue__ViewPortSize_WindowBorderless.zip](https://github.com/user-attachments/files/16511052/Issue__ViewPortSize_WindowBorderless.zip)


Start by running the provided minimal reproduction project on Godot 4.2.2 under Windows and compare viewport rendering, mouse coordinates, and screenshots before and after toggling borderless mode. Trace the window/viewport borderless handling and determine what needs to keep the rendered content and input coordinates aligned; done means the top content is not cropped or stretched and mouse positions match the display.

Written by the indexing model from the issue text.