Control inside Viewport inside ViewportContainer ignores gui-event tree order and is in front

[Reneator]

Godot version:
v3.3 stable

OS/device including version:
Windows 10

Issue description:

with a scene-structure like this:

The TextureRect is drawn in the right order (behind the button), but the TextureRect (set to mouse_filter_stop) catches all the mouse-inputs.
Therefore i cant click on the Button where the TextureRect is being displayed in the ViewportContainer:

In my game i have a world-map which is inside of a viewportContainer where the buttons block mouse-inputs even though they are not visible (either behind another UI-Element or even outside the viewport).
I have a complicated workaround for this in my project, but it still doesnt solve the basic problem of the button being in front.
The workaround checks if the mouse exits the viewport-container (as this control element is still properly handling the mouse-input) and switch the mouse_filter to Ignore for the buttons. But this doesnt work if the mouse is still inside of a button as it leaves the map:

I was expecting the texture-rect to have the same gui_input order as it is drawn (texture_rect is behind the button)

Steps to reproduce:
In the project the native behaviour is replicated. Run the project and see how the textureRect inside the viewport is actually soaks up the mouse-input as if it were in front.

Minimal reproduction project:
Viewportcontainer replication project.zip

[Calinou]

Related to #48368.

[dkaste]

I think I figured out why this is happening, but I'm not sure if I will have time to fix it.

See the following lines in Viewport::input() (linking Godot 4's code, but the same thing applies in 3):

if (!is_input_handled()) {
    get_tree()->_call_input_pause(input_group, "_input", ev, this); //not a bug, must happen before GUI, order is _input -> gui input -> _unhandled input
}


if (!is_input_handled()) {
    _gui_input_event(ev);
}

The code in the first block leads to SubViewportContainer::_input() being called, which in turn calls the child's own Viewport::input(). The child viewport then runs_gui_input_event(), which consumes the event. When the parent viewport exits _call_input_pause(), the event as already been marked as handled, so the GUI ignores it.

[akien-mga]

Duplicate of #39666