Using a native package gives so much more power - you define that the package relies on python, and maybe a mysql or postgres client, redis, whatever it needs, and then just install the one package, and let apt/dpkg handle the dependencies.
I'm a big fan of using the config-package-dev package from DebAthena to build config packages, which allow for about 99.9% of Debian server setup to be defined in Debian packages.