Agreed that Mycroft has performed far too clumsily for Mycroft over Moriarty, and his interview with John seems to serve the purposes of creating a Moriarity narrative for John to believe and act from, and giving him information to pass on to Sherlock. Which means John is being badly used by at least Mycroft if not both Holmes boys.
Now, I'll see your cheesecake and raise you my streudel: this is taking it far too far, but what if Sherlock taking a flatmate in the first place was part of a Holmesian plan all along because they realized they would need a patsy? Mycroft said they know about these people; Sherlock's job for his brother in ASiP then is to 1) get a name (for Moriarty, who could already have been on Mycroft's radar in a shadowy way) and 2) involve a third party who can be used to play out their game convincingly. Sherlock choses John, Mycroft vets him in the parking garage and agrees he'll do. Callous plan is then set in motion, for the greater good of the Commonwealth.
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What do 'real' people have, then, in their 'real' lives?
So we go round the sun; if we went round the moon, or round and round the garden like a teddy bear, it wouldn't make any difference.
The consolation of imaginary things is not imaginary consolation. -- Roger Scruton