Pakistan has recently signed Pak-Afghan transit trade agreement. This agreement (as I understand) means that Afghanistan can use Pakistani territory to import goods from any country, including India. It looks good on paper but in reality, if Pakistan is not careful, it can cause far reaching economical as well as security consequence for Pakistan. I believe working clauses are still to get agreed. I think there are economical and security consequence to this agreement, and we should discuss the consequences of this agreement keeping few things in mind.

1: Afghanistan is a landlocked country. Obviously we would not like that Afghanistan suffers because of being a landlocked country. Afghanistan is a neighbouring country and Pakistan should do whatever to help Afghanistan develop and grow, so that lives of Afghan gets better. Anyhow, this should not happen at the cost of Pakistan.
2: Pak-Afghan transit trade agreement is good for both countries, as when Afghanistan needs Pakistani territory to import their goods, Pakistan needs Afghanistan territory to export goods to central Asian countries.
3: Pak-Afghan border is very difficult to monitor, and practically it is open border for smugglers.
4: When transit goods go through a country than seepage of those goods in the country is not difficult, especially when country is not very organised and corruption in the country is rife (both is true with Pakistan).

Economical Consequence: Pakistan could not impose import duty on transit goods. So, large proportion of goods destined for Afghanistan could (and most likely would) seep into Pakistan duty free during transit and due to smuggling after reaching Afghanistan (if import duties in Afghanistan is less than Pakistan). Banned goods in Pakistan could also get to Pakistan using this process. Many goods that Pakistan exports to Afghanistan and Central Asia could get replaced by Indian cheaper goods, and that would harm Pakistani economy as well as industries.

Security consequence: Pakistan has unresolved Kashmir conflict with India, and relationship could not become trusting until this unresolved conflict is sorted out. It is unlikely that Pakistan would stop supporting Kashmiris fighting against Indian occupation, and in consequence, Indian would keep creating encouraging and supporting separatist and terrorist movements in Pakistan. That means, India could use transit trade facility to smuggle weapons, money and equipments to these elements in Pakistan whenever India would want to.

Solution: In my opinion, I think that even though Pakistan has signed Pak-Afghan transit trade agreement, they should include some self-preserving clauses in the agreement. These are:

1: Pakistan would not allow Pakistani territory as transit for Indian goods until all bilateral issue with India is resolved, including Kashmir (unless, such goods have been given special permission for transit).
2: Pakistan would not allow Pakistani territory as transit for goods that are coming from countries having no relationship with Pakistan (like Israel).
3: Pakistan would not allow Pakistani territory as transit for goods that has lower import duty in Afghanistan than Pakistan (to stop smuggling back into Pakistan).
4: Pakistan would not allow Pakistani territory as transit for goods that are banned in Pakistan (unless, such goods have been given special permission for transit).
5: Pakistan would not allow Pakistani territory as transit for goods that are coming from countries where Pakistani goods have restrictions.
6: All goods that would enter Pakistan would get inspected by Pakistan at port of entry for security reasons.