### 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)

if (get_base_window() == p_window) {
		gui_release_focus();
	}
}
bool Viewport::_gui_control_has_focus(const Control *p_control) {
	return gui.key_focus == p_control;
}
void Viewport::_gui_control_grab_focus(Control *p_control) {
	if (gui.key_focus && gui.key_focus == p_control) {
		
		return;
	}
	get_tree()->call_group("_viewports", "_gui_remove_focus_for_window", (Node *)get_base_window());
	if (p_control->is_inside_tree() && p_control->get_viewport() == this) {
		gui.key_focus = p_control;
		emit_signal(SNAME("gui_focus_changed"), p_control);
		p_control->notification(Control::NOTIFICATION_FOCUS_ENTER);
		p_control->queue_redraw();
	}
}
void Viewport::_gui_accept_event() {
	gui.key_event_accepted = true;
	if (is_inside_tree()) {
		set_input_as_handled();
	}
}
void Viewport::_drop_mouse_over() {