I’m not sure what you’re comparing that to. This project is about easily deploying your own app/side-project, which wouldn’t be available via apt.
At the end of the day if you use this tool I guess all you’d need to worry about (given the tool is stable and works obviously) would be apt upgrades of the OS and even that you can automate, and then just figure out your reboot strategy. For me, I don’t even want to deal with that, so I happily use fly.