Do you mean that the method might be overridden? If so, yes. The reasoning behind this is that if the code ends up invoking an override of ownerOf it will probably break pretty badly.
Nowadays, I think we should stop doing this and just use the unqualified (potentially overriden) function. Our policy anyway is that if a developer overrides a function with custom logic it is their responsibility to make sure that other things don't break. It's very difficult/impossible for us to write contracts that are customizable while at the same time making sure they stay internally consistent given arbitrary customizations.
A good option could be to separate the function we use internally from the function used externally, so that they could be overriden separately.
I don't like this approach because it's the kind of thing that can easily create confusion - there will be multiple functions for doing the same thing.
And there's also a contract size concern - it's not difficult to go over the 24kB limit.