The British position in Lord Wavell/Lord Mountbatten's time was that Kalat was like any other Indian princely state. Nevertheless, Lord Mountbatten mediated negotiations between M.A. Jinnah and the Khan of Kalat and Jinnah, on behalf of Pakistan, recognized Kalat as a sovereign, independent state. The question is - why did Jinnah adopt that position?
The answer has to do with the legal position of the Indian princely states. Under the Indian Independence Act, British paramountcy would lapse, and all treaties between the princely states and Great Britain would cease to have effect. However, all British Indian treaties with sovereign states would continue to be in effect, and be inherited by the newly independent India and Pakistan.
The British had obtained a perpetual lease of Quetta and surrounding areas from the Khan of Kalat. If Kalat was a sovereign state, then Pakistan would inherit that lease. If Kalat was a princely state of British India, the lease would lapse, and Quetta would revert to Kalat. Pakistan's claim on it would depend on whether the Khan of Kalat acceded to Pakistan or not.
Some of the evidence for this answer is presented below. It is in reverse chronological order.