Right now they were incorporated into the rest of Pakthun province from being a special federally administrated region. So on paper they are completely part of the country.
But on the ground yes their own set of rules and code is still much relevant. Tribal chiefs are mainly elected in the assembly, their own tribal courts have more value than actual courts etc
That is the history of that region. Even British used it mainly as a frontier with Afghanistan not wishing to establish their rule on it.
I don't really mind it you can't force someone to hug something, If they prefer their thousand years old tribal code more that shouldn't be an issue. Spain has similar kind of problems in some of it's regions, problem arises when you resort to violence to challenge the state which creates nothing but unnecessary deaths for everybody and doesn't achieve anything.
In that way situation is much better than 10-12 years ago it was really made worse by WoT since US drones killed people there and they turned on Pakistani govt for siding with US the reason TTP the Pakistani Taliban group were created, many have formally joined the state setup but some factions still remain at odds and reports are Pakistani govt is in talks with some of them who are willing to negotiate.
I'm totally for negotiations but there is one faction within them which used to run drug trade in those parts who carried out that attack on school killing 140 children in 2014, no matter what happened killing children is part of no tribal code or armed conduct. They should be brought to justice and they aren't willing to talk either.