I have a workaround for this, which is just using a tip from Jae Joon to me* from 3 years ago (!). Instead of setting the title offset as shown above, I set it in this fashion:
self.subplot.titleOffsetTrans._t = (0., 20.0/72.)
And then this somehow doesn't interact with the make_axes_area_auto_
One problem down. (I hope it is OK that I am answering my own questions, but didn't want to leave them out there and have others bother to work on it).