> 1. Python daemon threads

I think the answer is to document a bit more clearly that they can pose all kinds of problems.  Perhaps we could even display a visible warning when people create daemon threads.

> 2. Python threads created in atexit handlers

We could run the "join non-daemon threads" routine a *second time* after atexit handlers have been called.  It probably can't hurt (unless people do silly things?).

> 3. non-Python threads accessing the C-API

This one I don't know how to handle. By construction, a non-Python thread can do anything it wants, and we cannot add guards against this at the beginning of each C API function. I think that when someone calls the C API, we're clearly in the realm of "consenting adults".