Reading A&A, some diseases seemed to be caused by demons, faeries or other supernatural elements.
Which makes me wonder if these diseases need to penetrate, or if the mage simply makes a disease avoidance roll like everyone else.
I partly suspect the rule in this case might be a relevant Power is used, then penetration is checked then a disease avoidance roll is made- but that doesn't quiet fit hermetic guidelines.
The disease itself wouldn't need to penetrate, but the Power used to cause the disease would need to penetrate as normal. The victim may or may not get to make a disease avoidance roll, depending on the Power used.
See "Demons of Disease" in A&A p45, and "Decani" and the power Ride the Diseased Body in RoP:I p52 for examples of how demons can cause diseases.