### 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.dragging) {
			
			Control *drag_preview = _gui_get_drag_preview();
			if (drag_preview) {
				drag_preview->set_position(mpos);
			}
			gui.drag_mouse_over = over;
			gui.drag_mouse_over_pos = Vector2();
			
			
			Viewport *embedder = nullptr;
			Vector2 viewport_pos;
			if (is_embedding_subwindows()) {
				embedder = this;
				viewport_pos = mpos;
			} else {
				
				Window *w = Object::cast_to<Window>(this);
				if (w) {
					if (w->is_embedded()) {
						embedder = w->get_embedder();
						viewport_pos = get_final_transform().xform(mpos) + w->get_position(); 
					}
				}
			}
			Viewport *viewport_under = nullptr;
			if (embedder) {
				
				for (int i = embedder->gui.sub_windows.size() - 1; i >= 0; i--) {
					Window *sw = embedder->gui.sub_windows[i].window;