Differences between advanced project manager download & a downloaded zip config

I wanted swap our primary config (a dowloaded zip) with a copy of the game_demo config,
Because our Primary files indicate it comes from the VFX defaults and we are a game studio.

There are differnces between advanced project manager download & a downloaded zip config

When I download a game demo config via advanced project manager I get this

game_demo/cache/
game_demo/config/
game_demo/install/
game_demo/tank
game_demo/tank.bat

When I download a config as a zip file from the Pipeline Configuration Page, I get this:

zip/core/
zip/env/
zip/hooks/
zip/icons/
zip/.cached_metadata.pickle
zip/.pre-commit-config.yaml
zip/after_project_create.py
zip/azure-pipelines.yml
zip/icon_256.png
zip/info.yml
zip/LICENSE
zip/README.md

The Zip for Primary appears to be only the contents of the game_demo config folder,
but game_demo comes with cache, install, app_store, tank, etc.

I am confused by these differing hierarchies.
can anyone clarify this?

Only the config folder is normally managed. The rest are created at runtime.
The project directory will look like yourproject/config/ yourproject/install, etc. where config could come e.g. from git.
The advanced project setup takes a reference to a config directory/zip. The rest are created by the setup script.