### 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(nullptr);
	ERR_FAIL_COND_V(!is_inside_tree(), nullptr);
	if (!get_parent()) {
		return nullptr; 
	}
	return get_parent()->get_viewport();
}
void Viewport::set_embedding_subwindows(bool p_embed) {
	ERR_THREAD_GUARD;
	gui.embed_subwindows_hint = p_embed;
}
bool Viewport::is_embedding_subwindows() const {
	ERR_READ_THREAD_GUARD_V(false);
	return gui.embed_subwindows_hint;
}
void Viewport::subwindow_set_popup_safe_rect(Window *p_window, const Rect2i &p_rect) {
	int index = _sub_window_find(p_window);
	ERR_FAIL_COND(index == -1);
	SubWindow sw = gui.sub_windows[index];
	sw.parent_safe_rect = p_rect;
}
Rect2i Viewport::subwindow_get_popup_safe_rect(Window *p_window) const {
	int index = _sub_window_find(p_window);
	ERR_FAIL_COND_V(index == -1, Rect2i());
	return gui.sub_windows[index].parent_safe_rect;
}
void Viewport::pass_mouse_focus_to(Viewport *p_viewport, Control *p_control) {