This is an exercise in the fancy new science of
Macroprudential regulation.
The point isn't to stop buy-to-let mortgages, or even to limit them most of the time. It is to limit them only at those times when the market is out of shape and the only alternative would be to meddle with interest rates.
Some might argue that it isn't a great plan because it requires central bankers to be godlike geniuses, and it lets politicians off the hook for failures to reform planning and zoning regulations. But it has some rationale in that the alternative distorts monetary policy to cover those same failings, which is probably worse.