### 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 (p_disable == disable_input) {
		return;
	}
	if (p_disable) {
		_drop_mouse_focus();
		_drop_mouse_over();
		_gui_cancel_tooltip();
	}
	disable_input = p_disable;
}
bool Viewport::is_input_disabled() const {
	ERR_READ_THREAD_GUARD_V(false);
	return disable_input;
}
Variant Viewport::gui_get_drag_data() const {
	ERR_READ_THREAD_GUARD_V(Variant());
	return gui.drag_data;
}
PackedStringArray Viewport::get_configuration_warnings() const {
	ERR_MAIN_THREAD_GUARD_V(PackedStringArray());
	PackedStringArray warnings = Node::get_configuration_warnings();
	if (size.x <= 1 || size.y <= 1) {
		warnings.push_back(RTR("The Viewport size must be greater than or equal to 2 pixels on both dimensions to render anything."));
	}
	return warnings;
}
void Viewport::gui_reset_canvas_sort_index() {