This is a question that has come up many times, and i have asked Jobo Germany about this and have no clear answer.
It appears that this was part of the original programming, but never got implemented. It is after all a fairly simple thing.

This guy hacked the ATL 1000 chip and kind of made his own custom process:
http://photo.net/film-and-processing-forum/00bZqn

From what he told me and i think that is also in the text, there is no way to adjust the main sequence of the process, including the temperature and main water bath fill - maybe this can be done with some more programming knowledge or tinkering.