### 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 (!gui.tooltip_control) {
		return;
	}
	
	Control *tooltip_owner = nullptr;
	String tooltip_text = _gui_get_tooltip(
			gui.tooltip_control,
			gui.tooltip_control->get_global_transform().xform_inv(gui.last_mouse_pos),
			&tooltip_owner);
	tooltip_text = tooltip_text.strip_edges();
	if (tooltip_text.is_empty()) {
		return; 
	}
	
	if (gui.tooltip_popup) {
		memdelete(gui.tooltip_popup);
	}
	if (!tooltip_owner) {
		return;
	}
	
	PopupPanel *panel = memnew(PopupPanel);