The ISI absolutely ran (and probably still run) training camps, some of which are Al Qaeda. But during the 80’s and 90’s it was with CIA money. As a side note, many of those trained with CIA money were then sent by the ISI to Kashmir to fight the Indians.
Many other groups (Saudi Arabia, Bin Laden, etc.) also funded training camps.
The northern part of Pakistan and the southern part of Afghanistan are farily well integrated both ethnically, culturally and linguistically, and the border between the two countries might as well not even exist in some places. It’s true that the Taliban originated in Pakistan and is taking refuge there even now. But al Qaeda is a distinct orgnanization, and bin Laden has publicly taken credit for the 9/11 attacks. So, when you say “Pakistan” what specifically do you mean?