Quite simply, my arduino projects last a long time, and get passed on from year to year to different people. Source code get's lost, or deleted. In academia, students are quite bad about keeping things consistent from year to year. So, it's far more convenient to have it stored on the device, just as it would be on a PLC. The ability to come back 3 years later, and download the source material from the dvice, modify, expand it what have you, and then upload it back from the same IDE is very convenient and saves many headaches.