Is it permissible to deal with a company that pays for goods I purchased from outside the country, and then I repay the amount to it after two months with a 6% commission, knowing that the commission increased by 1% due to not paying in cash?

If the company pays the price of the commodity on your behalf from its own funds, and then collects from you what it paid along with taking a percentage, such as 5%, then this is usurious interest (riba), which is forbidden, and calling it "expenses" does not make it permissible. Scholars have unanimously agreed that every loan in which an increase is stipulated is usury (riba).