### 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_MAIN_THREAD_GUARD;
	if (gui.subwindow_focused) {
		gui.subwindow_focused->push_text_input(p_text);
		return;
	}
	if (gui.key_focus) {
		gui.key_focus->call("set_text", p_text);
	}
}
Viewport::SubWindowResize Viewport::_sub_window_get_resize_margin(Window *p_subwindow, const Point2 &p_point) {
	if (p_subwindow->get_flag(Window::FLAG_BORDERLESS) || p_subwindow->get_flag(Window::FLAG_RESIZE_DISABLED)) {
		return SUB_WINDOW_RESIZE_DISABLED;
	}
	Rect2i r = Rect2i(p_subwindow->get_position(), p_subwindow->get_size());
	int title_height = p_subwindow->get_theme_constant(SNAME("title_height"));
	r.position.y -= title_height;
	r.size.y += title_height;
	if (r.has_point(p_point)) {
		return SUB_WINDOW_RESIZE_DISABLED; 
	}
	int dist_x = p_point.x < r.position.x ? (p_point.x - r.position.x) : (p_point.x > (r.position.x + r.size.x) ? (p_point.x - (r.position.x + r.size.x)) : 0);
	int dist_y = p_point.y < r.position.y ? (p_point.y - r.position.y) : (p_point.y > (r.position.y + r.size.y) ? (p_point.y - (r.position.y + r.size.y)) : 0);
	int limit = p_subwindow->get_theme_constant(SNAME("resize_margin"));
	if (ABS(dist_x) > limit) {
		return SUB_WINDOW_RESIZE_DISABLED;
	}