I think part of this is actually just a failure of capability.
Point (1) and (2) can be true, while (3) only applies if asked. If not asked, it doesn’t evaluate whether it would result in humanity being destroyed (or a database being deleted). It is not capable of correlating the knowledge that it has without specifically aiming to do those correlations.
Humans also do this all the time, of course.
That said, I would generally think of a superintelligent entity as being more coherent in what it knows, in the sense that at least all the reasonably obvious and relevant correlations are taken into account and used to predict evaluate actions before acting—even when not specifically asked about each of them.
That may be oversimplified though, since I would also expect a superintelligent entity to consider a great deal more things “reasonably obvious”. The space of “obvious correlations” between them all likely grows much faster than the number of obvious things themselves, which could mean that it is exponentially difficult to take them all into account.
So maybe it is not practically possible to be both superintelligent and coherent in this fairly strong sense.
I really don’t like seeing 20 top-level posts from the same author within 30 minutes, but maybe there are extenuating circumstances like having them pre-written offline over a few days and just regained Internet access to post them.