Is it permissible for an employee working in a company warehouse that sells a specific product to sell to customers who previously came through the company's agents, and receive a commission on these sales, especially if he offers the customer a better price than the price they get from the agent?

There is no harm in directly selling the employer's goods to customers and taking a commission for it, even if these customers have previously dealt with the company's representatives, provided that the employer authorizes it. The criterion for the permissibility of the transaction and taking the commission depends on the company's knowledge and permission.