Counterpoint: The MVP is usually what ends up in production. If your code is a heap of garbage but chocolate-coated on the outside, you're gonna impress management and they'll want to push it live asap. Then the issues start exploding.
"I actually like having visible directories, versus having to figure out where in /usr/share or /usr/local/ or ~/.local or /var an installer chose to sneak their files in."
You seem to be mixing together two concepts here: