Basil has also said that he is extremely old. So there's a question of whether the code would have been one recent enough to be recognized by Penny or any hundreds of factors. And honestly, for an AI to be organic enough to change over time, it would have to have some capacity to change some of it's coding on it's own, otherwise it'd be the same artificial entity it was created as. So those thousands of years(Basil did say he was alive for thousands of years, right?) that Basil was alive, he very well could have rewritten his own code so that it was unrecognizable as Mengasi. I mean, obviously the fact that he's okay with killing Artemis, the possibly last Mengasi can't be something he was programmed with.