This SAME entity then also needs the ability to cure cancer. To me, adding abilities like this incurs complexity penalties on a pretty big scale.

This says that if you are, say, an Inca ruler and you hear about Spanish conquistadors, the fact that they can ride weird beasts AND shoot fire out of metal sticks AND do a lot of other supernatural-looking stuff implies that you should disbelieve their existence -- probably not a good idea.

In general terms, the complexity penalties you're are talking about are justified only if these different abilities are unrelated. But if, instead, all of them have a common cause (e.g. massive technological superiority), the penalties no longer apply.