The character creation software in question is the Shadowrun Fourth Edition data file for Lone Wolf Developments' Hero Lab software.
Here is what one of my friends has said on the matter:
"Encephalon should certainly be included, no matter what interpretation you use of Matrix vs. normal attributes and how modifiers for them carry over. It specifically uses the term "Matrix Tests", directly contradicting whoever it was you were emailng. There is a case to be made that Rating 1 should be included and Rating 2 shouldn't, because the rating 2 bonus is conditional on being in AR or VR and Herolab doesn't generally include conditional bonuses."
"EPE: Pushed would be included depending on your interpretation of the attributes issue. I'm going to include it in my game with the optional rules on pg. 226 SR4A for capping hits with Logic. Normally, Logic has no bearing on Matrix Tests whatsoever, so why would hacking receive benefits from a Logic boosting augment?"
"Neo-corticals: Again, this is situational, i.e. you can't be under stress. Which is basically all in-session hacking after the legwork is over. It would also be caught up in the interpretation of attributes argument, so in Herolab's interpretation probably wouldn't apply."
"If that is how they are interpreting Logic via Matrix Tests, I don't really see an argument you could use to change their mind. SR4A specifically says that Matrix Tests are divorced from the normal attribute+skill link and gives optional rules on how to play it otherwise. Still, Herolab should be including Encephalon certainly, but not the others RAW."
I could still use some clarification and assistance with this issue.