The NGO delivery channels are privileged because they are charitable. That's why they get to bypass the country's restrictions. You can't open that channel up, the country would object at humanitarian exemptions being used as a backdoor for commercial imports.
What I mean is that they should use the standard commercial channels and use their economical and political channels to make sure they work well so that everyone would profit from having working import systems.
The result of this might be NGO money being used to fund inefficiency or even corruption. By maintaining their own channels, the NGOs can be more certain their funds are being used responsibly. It's possible otherwise local government would take it upon themselves to try to bleed these western NGOs.
If you read the article you would know that the problem wasn't finding the money to pay import duties (or the delivermen), the problem was not being allowed to give them the money in the first place and the sheer informality of the logistics infrastructure.