Sure, “British citizenship cannot be conferred on any person at the Queen’s personal whim.”
But the British Nationality Act was an act of Parliament, right? So, if the Queen wanted an individual to be created a British citizen, surely she could ask Parliament to pass an act making that sets aside the BNA in the case of that individual, and grant him citizenship without his meeting all the normal requirements.
The Queen could “make it known” that she would be in favour of such an amendment to the Act, but it would have to be proposed as a Bill by an MP and go through the same procedure of discussion as any other Bill.
In a case like this one I suppose the Bill might make it through the parliamentary process easily enough, but I can’t believe it would be worth all the hassle just so Jack Ryan could have a pointless title.
Having said that, the nationality rules were bent to allow Zola Budd to appear in the 1984 Olympics, so my guess is that they’d take his word for it about the residency intention and then conveniently overlook that he never came back afterwards. Everybody would come out of it looking like jerks though, which seems to contradict the whole point of the exercise.