Musharraf has pledged to turn the "A" Agencies into "B" Agencies and operate freely. Well that is so much loose talk, he knows the Baloch are a fierce enemy in a very harsh land and his military lacks the ability and determination to fight the Baloch, much less dig out bin Laden who is paying big money for the rat hole he's in.
Meanwhile Musharraf can't even militarily face the madrassas cranking out hundreds of terrorists each month. Pakistan is the center of world terrorism and that won't change until Musharraf's dead and we garrison Pakistan. There will be another 9/11, probably an attack on our homeland again, in my opinion, a public ferry. Too many nut-case, freak Muslims and they are all going to Pakistan.
The double layer sovereignity you mention is a fact, with a major caveat of which more later.
It does not apply to Balochistan. Balochistan is not an Agency but instead a Province.
The Agencies are what is collectively called Federally Administered Tribal Agencies (FATA) and include Khyber, Mohmand, Bajaur, Kurram, Bannu, Khar , North Waziristan etc.
On double layer sovereignity the use of the term Federally Administered would suggest they are not as sovereign as made out (wink).