Your late arrival does not provide you additional benefits at the time of checkout, it is not like a restaurant that the table can take additional guests who would leave before your arrival.

However I would recommend that you talk to the owner, inquire if they have another guest the same day of your checkout, and if so, if he knows the time they would arrive. From your original post, some locations have only late flights and therefore late arrivals.

Also request the owner to allow you to check out offering to throw the towels and sheets in the washer and dryer, which are the most time consuming tasks for the housekeeper.

Finally, even if you negotiate a modest late check out fee, you may work out a deal where you could stay in the public areas of the house while the housekeeper cleans the inside of the home.

Hope these ideas will give you options at the time of negotiations.