Pakistan supported Ahmed Shah Masoud in the 1970s against Daud Khan. However, as usual Pakistan backstabbed and started supporting that nutcase Hekmatyar (this move alone is why Kabuli Tajiks don't trust Pakistan as Hekmatyar caused maximum damage firing RPGs in the middle of Kabul leading to 30K casualties in the first half of the 90s).
Then Mullah Omar arose and we all know what happened after that. Northern Alliance was seen as more pro-India and places in FATA especially Waziristan was the second home to the Haqqanis. Quetta was the makeshift base for the Kandaharis. Remember when I said before Waziristan always came to Afghanistan's rescue and aided it during the Anglo-Afghan war and other internal turmoil previous Kings had.
War on Terror, GHQ probably ran a cost reduction analysis and realized having Taliban in power is more beneficial than having Ashraf Ghani and Karzai in power. Ghani had open bases and training fields for BLA in Kandahar during his time. Not to mention during the early NDS early days it was majority Panjsheri. So at that moment in time they thought it was good.
I think its probably more of a "killing 2 birds with one stone" thing. If you have Pashtuns in power in Afghanistan and are friendly with you, you'll check 2 boxes and don't ever have to worry about the Western border again and focus on Kashmir.
Like usual no long term planning is done and everything is done on the whim since our instituitions are weak. In the documentary Waziristan Hard Homecoming by Russia TV (this was shot in Raheel Sharif's era) the army was bragging about high tech cameras and motion sensors along the border. However, when the border fence was finally commenced it had none of that and it was completed via lots of corruption of the materials that were used to make the fences.
