ScrollContainer doesn't obey content margins, margin container or clip rects

### Tested versions

v4.2.2.stable.mono.official [15073afe3]

### System information

Kubuntu 22.04, X11, RENOIR AMD Ryzen 5700G with radeon Graphics.

### Issue description

Godot's Scroll Container UI Nodes don't obey margins from style flat and margin containers also it doesn't obey their clipping rect when clip contents is on.

### Steps to reproduce

- Download project
- open tile-_editor.tscn
- mess around with scroll container and the grid of magenta buttons
- mess around with the theme if needed
- see that it's not being clipped properly

### Minimal reproduction project (MRP)

[Quest.zip](https://github.com/user-attachments/files/15997011/Quest.zip)

Open the attached Quest.zip project and reproduce the issue using tile-_editor.tscn. Check the ScrollContainer with the grid of magenta buttons and its theme, focusing on style-flat margins, MarginContainer margins, and clipping when clip contents is enabled. Done means the content respects the configured margins and clipping rectangles.

Written by the indexing model from the issue text.