Is it permissible to sell a commodity to a company, with the company setting a minimum price, and then sell it at a higher price while giving the company the specified price and secretly taking the surplus?

It is not permissible for an agent to take the increase for himself; rather, it is the right of his principal. If the company has authorized you to sell its goods, then you are its agent, and whatever you sell for more than the price set by the company, the increase belongs to the company. If you take the increase without the company's knowledge, this is not permissible. If selling is not part of your primary job, it does not permit you to take any of its money without its permission. You can stipulate to the company that you receive a fee for your service, or agree with it that any amount exceeding the specified price is yours.