What I'd look to do in this situation would depend on whether "arrive home Friday morning" means:
a) My flight lands at 11:48pm Thursday, but with time spent exiting the airport and getting home I don't enter my residence until 12:40am Friday.
b) My flight lands at 12:05am Friday.
c) My flight lands at 6:30am Friday.
In situation (a) I could see the company's argument for Thursday being the last day of travel, though I think it's easy to argue that Friday is the last day because merely being at the airport is not being "home".
In situation (b) it's clear that Friday technically is the last day of travel though I could imagine some managers or finances staff thinking I'm gaming the system with a technicality.
In situation (c) there should be no argument about Friday being the last day of travel. If my employer gave me grief about it I would cease flying red-eyes and explain to my project manager that's why I need to leave the job site at noon on Thursday. After all, "I don't make the rules, I just follow company policy."