Do you mean that small area where the paddle attaches? It's about as big as a quarter? Regular warm water has always cleaned mine out, it's just baked dough and loosens right up. I can wipe it out with a paper towel, but then I've never let it go for long either. I think my machine does not recommend water in the pan for over twenty minutes, probably because it may affect the integrity of the seal that keeps water from leaking out.
And me personally, I wouldn't worry about germs any more than I would clean out the toaster everytime I used one. It's just baked dough and everything will heat up again to a high temp next time you use it.
If it's what I'm thinking about.
Give us this day our daily bacon.