Depends on your target. 4000 pen is statistically better in % damage increase IF you are not overpenetrating and IF you are not attacking shields (You're talking around a 8-9% dmg increase for the pen, vs roughly 5% dmg increase for automaton depending on your build). You must also take into consideration that Automaton won't count on non-physical damage such as poison injection (I'm assuming you're a stamsorc, something like a NB is going to have a lot more to consider with incap/killer's blade). Personally my most difficult targets tend to be magicka sorcs, so that would lean me towards automaton in this comparison.