Transit fees are likely to be reasonable, as this is an agreement which ensures the protection of goods and establishing a forum for discussing fair trade policies. If the Tajiki are serious about expanding trade to 500m then the logical thing would be to work with the Chinese and expand their current highway network to connect with Chinas G314 motorway which is already built very close to the Tajik border and runs straight into Gilgit.
The Afghans dug themselves into a hole really, they keep on trying to destroy Pakistani relations and keep maintaining animosity despite our multiple attempts to have friendly relations, they also have stopped trade at the Tajik border several times which likely concerns the Tajik government.
I think that Tajikistan will be OK with having longer transit times if it means their goods will eventually reach their destination, whereas with the Afghan route its unknown if they suddenly start getting emotional and shut the trade route, or if Pakistan completely closes the border.