Charge per hour, that is always the best. If you already have an established cleaning company, charging per hour is the best you can do. This will make things a lot easier for the restaurant or any company that hires you. You can always call your competition and ask for a quote to see how much they're charging and adjust depending on that.
What I would charge would partly depend on what products I was using and the flooring type.
I had a 1500 sq ft commercial kitchen with a tile and grout floor.
Tried Greased Lightning, Steam Cleaning on the flooring but the product that worked the best and also made the customer very pleased was an Enzymatic Product 1 was super floor degreaser--90.00 a gallon. Did 1 deep floor scrub using super floor degreaser vac'd or mopped up the residue liquid.
After the floor scrub all we had to do was vac the flooring and mop with the super floor degreaser-- no pushing residue liquid to the floor drains, no vacing up liquid. The enzymatic "eats the food grade grease" and then evaporates into the air.
We found a similar product for w a y l e s s $$.
Brad BD Janitorial