### 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.sub_windows.size() < 2) {
		return;
	}
	if (!gui.sub_windows[gui.sub_windows.size() - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
		int index = gui.sub_windows.size() - 1;
		while (index > 0 && gui.sub_windows[index - 1].window->get_flag(Window::FLAG_ALWAYS_ON_TOP)) {
			--index;
		}
		if (index != (gui.sub_windows.size() - 1)) {
			SubWindow sw = gui.sub_windows[gui.sub_windows.size() - 1];
			gui.sub_windows.remove_at(gui.sub_windows.size() - 1);
			gui.sub_windows.insert(index, sw);
		}
	}
	for (int i = 0; i < gui.sub_windows.size(); i++) {
		RS::get_singleton()->canvas_item_set_draw_index(gui.sub_windows[i].canvas_item, i);
	}
}
void Viewport::_sub_window_register(Window *p_window) {