Yes, you can make changes in the Project Settings dialogue in production, and any changes you make there will be made to production immediately. Apptio (at least, in R12) will prompt you with a warning that you are making a change directly to production, and you will need to confirm your changes again. I would advise against this, though, as making changes directly to production does not allow you to test the changes and make sure they haven't affected anything within the project. I suggest you make your changes in development, perform regression testing, and then check in (for auto-promotion to staging) and promote to production when you're sure the changes didn't compromise your project's integrity.
Some changes you need to make directly to production (e.g., default time period), but even with these changes, I would suggest making them in development first, testing them, and only then making the same change in production.