Is it permissible to add a sum of money to the price of a commodity when buying it for a customer, along with taking a fee for transportation, food, and device programming? And is repentance sufficient to erase the sin in case of not knowing the Sharia ruling?

If the buyer is acting as an agent for the customer, it is not permissible for him to take an amount exceeding the real price unless his principal knows and approves. He must repent for what he took in the past and return the excess money to its owners by any possible means, or ask for their forgiveness. Al-Ghazali mentioned in "Minhaj al-Abidin" that repentance from financial sins is by returning the money if possible, or seeking the owner's absolution if that is difficult, or giving charity on his behalf if he is absent or deceased, or by increasing good deeds and supplicating to Allah to appease the rightful claimant on the Day of Judgment.