A fully isolated virtual machine means Phoenix.new’s fingernails can get arbitrarily dirty. If it wants to add a package to mix.exs, it can do that and then run mix phx.server or mix test and check the output. Sure. Every agent can do that. But if it wants to add an APT package to the base operating system, it can do that too, and make sure it worked. It owns the whole environment.
This offloads a huge amount of tedious, repetitive work.