### 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)

ERR_READ_THREAD_GUARD_V(false);
	return use_xr;
}
void Viewport::set_scaling_3d_mode(Scaling3DMode p_scaling_3d_mode) {
	ERR_MAIN_THREAD_GUARD;
	if (scaling_3d_mode == p_scaling_3d_mode) {
		return;
	}
	scaling_3d_mode = p_scaling_3d_mode;
	RS::get_singleton()->viewport_set_scaling_3d_mode(viewport, (RS::ViewportScaling3DMode)(int)p_scaling_3d_mode);
}
Viewport::Scaling3DMode Viewport::get_scaling_3d_mode() const {
	ERR_READ_THREAD_GUARD_V(SCALING_3D_MODE_BILINEAR);
	return scaling_3d_mode;
}
void Viewport::set_scaling_3d_scale(float p_scaling_3d_scale) {