Mouse reaction conflict between control nodes and 2D viewport

[ca3games]

Godot version:
Godot 3.2.2 win 64

OS/device including version:
Windows 10 x64 (Vega 8 with Ryzen 3)

Issue description:
The control nodes stop reacting when there's a viewport 2D scene.

Steps to reproduce:
Create a Basic GUI, make a 2D scene.
Create a Viewport, add the 2D scene.
Control nodes on the parent scene will stop working.

Minimal reproduction project:
Editor (GUI).zip

There's two scenes (bugged scene and non bugged scene).
Use the two to compare, specially on the bugged scene, click on the center right checkboxes, they don't work, they only work when you click Import Sprites, hit cancel, then the 2D scene inside the viewport dissapears and the checkboxes works.

[Sauermann]

In your MRP, the Control BODY in the SubViewport accepts the events, that you are missing in the main viewport.

This is a duplicate of #39666.