Is there a problem here? I haven't heard of anyone even wondering about this before. threading.py worries about Threads created _by_ threading.py, plus the magical (from its point of view) thread that first imports threading.py. Users mix in `_thread` threads, or raw C threads from extension modules, essentially at their own risk. Which risks are minimal, but can have visible consequences.
I don't view that as being a real problem. It might help if, e.g., a Wiki somewhere spelled out the consequences under different Python implementations (while I don't know for sure, I _expect_ the current docs just say "in normal conditions, the main thread is the thread from which the Python interpreter was started" because it doesn't want to over-specify the behavior in an area nobody really cares about).