More importantly, Pashtuns aren’t really Afghans. A great many of them live in Pakistan and most of them think of themselves as Pashtun before Afghan or Pakistani.
The author sort of dances around this, but there is a good reason why Pakistan originally supported the Taliban.
If Pashtuns focus on Pashtun nationalism, it requires disassembling the Pakistani state so there can be a Pashtun nation-state.
If Afghan Pashtuns can be encouraged to focus on their Islamic rather than Pashtun identity, maybe they’ll go try to take over Afghanistan and run it under sharia instead.
Actually there are something like 25M Pashtuns in Pakistan (about 16% of the population) as compared to ~13M in Afghanistan.
The author seems to be saying that Pastun culture has a historic inclination to resist outside interference from those attempting to impose anything on the Pastuns. I assume he includes sharia and the taliban in those interfering forces.