Is it permissible for employees to be paid an amount higher than the actual cost of their hotel accommodation if the company sets a ceiling for the amount allocated for the hotel and allows them to choose a less expensive hotel while keeping the difference?

The reference for the ruling on benefiting from these sums of money goes back to the company's terms and conditions. If the company gives the employee an allowance for what he actually spends on food and accommodation, and does not approve of this money being used for anything else, then it is not permissible for the employee to take more than what he spends. However, if the company gives him this money as a right for him to dispose of as he wishes, then there is no harm in him benefiting from the surplus money.