Tell me, where am I right now? I traveled there recently.
Governments certainly can find out that information, as my recent flights are recorded in lots of databases accessible to the. But it's much harder for non-government entities not directly involved in the travel to find this out due to privacy laws (particularly in the EU).
The pilot could eject at any time. Still dangerous, but more of a debugging session to avoid other similar costly in the future than a Hollywood-like "if we don't solve this now the pilot dies"