Pretty sure the computer won't adjust. There's a reason most people run programmers when making power modifications. As stupid as the bend in the piping seems, the engineers make everything a certain way for a reason. I'm not surprised in the slight loss in mpg.
They didn't design it like it is stock for any other reason than manufacturing cost and ease. Crushed pipe is easier and cheaper. It hurts performance, the computer would adjust if there is a change in the amount of air flowing in and out of the engine. If the exhaust breathes better, there will be more flow and it will start to run lean(more air), this will be picked up by the O2 sensor and it will adjust and add more fuel to try to get back to the proper A/F ratio. It's a minor change, I wouldn't have expected much mpg difference, but it should definitely not get worse. Some of it may be driving habit change...