What is the ruling on a Libyan transportation company submitting a proforma invoice to a company for the cost of travel to Tunisia, given that the travel was by private car and the company accepted the invoice?

If you explained to your employer that you traveled by your private car, and that the submitted invoice is an estimation of travel costs, then there is no issue in taking the compensation; because you did not deceive them. Whether the invoice matches what you spent, or is more because it is a donation from them with their knowledge, or if they give the value of a travel ticket regardless of the mode of travel, there is no sin upon you in benefiting from what they gave you.