The history of the Subcontinent has been of fiercely independent states rising up in rebellion of any empire that tries to keep them under its rule. The diversity of the people, stemming originally from their various ethnic origins (all the way back to the days of Harrapa and The Aryan invasion), belies a loyalty to ones kin above all else.
To Quote a Pakistani Pashtun saying I remember from a old news article:
"There is a famous Pakistani Pashtun quote: "I am a Pakistani for 50 years, a Muslim for 1,500 years and a Pashtun for 5,000 years.""
https://www.cbsnews.com/news/ancien...jewish-community-once-thrived-in-afghanistan/
The question you should not ask is will these 3-4 Million Afghanis born in Pakistan over the last 40 years be loyal to Pakistan? Why are the current 30-40 million Pakistani Pashtuns loyal to Pakistan? For all intents and purposes, the 3-4 million Pakistan born Afghanis are Pakistani in all but Identity card. They know more of Karachi then Kabul or Kandahar.
If they marry Afghans from their ancestral tribe, and bring them to Pakistan, and have "Afghan" babies, What will These babies say they are, if They go to Pakistani Schools, are included in every way in the Culture, and are on equal footing with their neighbors. Remember, our cultures are not all that different as those of say the US and Mexico where you can see 2nd and 3rd generation Mexican Americans are assimilating when holding legal status. Children of Illegal Mexican Immigrants stay in the shadows, and their children, having grown up in fear, don't assimilate.
This is why "naturalizing" these Children of Afghan Refugees, born in Pakistan, at the very least will change the whole dynamic. It is like a second migration to the Land who's meaning is suppose to be La ilaha illallah. Also if you are afraid they will stay "tribal", Then the government can study the success stories and compare them with the stories of failure. see what has worked. Where did Assimilation work, and where did it fail. For the time being, give these people, born in Pakistan some kind of Legal status, so they can seek an education, health care, and employment on equal terms.
Here is a couple videos on Mexican American Assimilation for comparison