Considering the time frame and rush to get the Avanti into production...it's likely no more than simply a quick way of solving a problem...find space for a battery. The engine is tight enough and using the 3EE battery simply was the cheaper and easy way out. Once they transitioned to the Group 24 battery for the '64 model year after incorporating it into the redesign of the front it made for much more versatility in battery selection by the factory and by consumers. That being said...the engine bay changes for the Group 24 battery do make a tight area even more so. If only someone at Studebaker had thought of locating the battery in the trunk it could possibly have made for a more logical radiator/belt drive design for the car...maybe even incorporating a/c with the supercharger from the factory.
But...as out of the box forward thinking as the Avanti design was...the Studebaker mindset was stuck in what they most knew and could afford...traditional thinking.