Is it obligatory to inform the restaurant owner about food and simple items that were given without his knowledge, or is it sufficient to waive my financial dues?

It is not permissible to dispose of another person's property without their permission. You must return the right to the restaurant owner or seek their forgiveness. There is no need to inform them of the exact nature of the act, but rather to estimate the right and return it. There is no problem in waiving your established rights with the company in exchange for what you disposed of, as long as the value of your right is not less than what you disposed of.