> Using set_wakeup_fd would fix them... except that it generates spurious warning messages when the wakeup fd buffer is full, and there's no way to stop it

Are you using a pipe or a socket to set_wakeup_fd?  Pipes have rather small buffers.  In any case, since, as you mention, Tornado and Twisted use it, and they never complained, perhaps your example is too contrived or artificial.