### Godot version

v4.2.dev.custom_build [60f3b7967]

### System information

Debian Linux X11 Xfce

### Issue description

Physics Picking within a `SubViewport` happens with `InputEventMouse` even when mouse events are disabled via `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`

The problem is that passive hovering still happens in the `SubViewport` with `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`.

I assume that it is a regression from #78017.

This was initially reported as a side-effect in #79271, which got closed, because the main issue was resolved.



### Steps to reproduce

1. Load and run MRP
2. move mouse over Icon

I would expect, that the `Area2D` receives no `InputEventMouse`, however it gets `_input_event` and also mouse-entered and mouse-exited signals.

### Minimal reproduction project

[IgnorePassiveHover.zip](https://github.com/godotengine/godot/files/12044510/IgnorePassiveHover.zip)

#ifndef _3D_DISABLED
	if (!use_xr) {
#endif
		if (p_allocated) {
			RS::get_singleton()->viewport_set_size(viewport, size.width, size.height);
		} else {
			RS::get_singleton()->viewport_set_size(viewport, 0, 0);
		}
#ifndef _3D_DISABLED
	} 
#endif
	_update_global_transform();
	update_configuration_warnings();
	update_canvas_items();
	for (ViewportTexture *E : viewport_textures) {
		E->emit_changed();
	}
	emit_signal(SNAME("size_changed"));
	Rect2i limit = get_visible_rect();
	for (int i = 0; i < gui.sub_windows.size(); ++i) {
		Window *sw = gui.sub_windows[i].window;
		Rect2i rect = Rect2i(sw->position, sw->size);
		Rect2i new_rect = sw->fit_rect_in_parent(rect, limit);
		if (new_rect != rect) {
			sw->set_position(new_rect.position);
			sw->set_size(new_rect.size);
		}
	}
}
Size2i Viewport::_get_size() const {