I'm all in favour of the idea of greater granularity for running doctests. However, as Malcolm rightly points out, doctests already provide a multi-file option through the __tests__ dictionary. The Django test runner should supplement, not replace this approach.
Invoking parts of a __tests__ dictionary would certainly be a valuable contribution, but it doesn't completely solve the problem. Doctests can be defined inline on a method or class (the classic sense of a doctest); it would be nice to be able to invoke these individual tests, too.
I'll mark this as accepted, but for the concept, not the provided implementation. I've updated the ticket to better reflect the accepted idea.