in costum process all kind of goods will have the same treatment (According to the term of deliveri), the different is the cost in each country.
The only cost which can be paid at the loading port is THC (terminal handling charge), and this will be mentioned in the bill of lading as THC prepaid.
Shipping lines usually applied the minimum charges, mean that you will have to pay the minimum cost if your cargo has less cost than their min. standard.
There is no reason for them to slow down the costum process. You can argue with them if there are some extra storage cost at port of destination.
Yes, you will be charged for those items.