You can customize the basic look and feel without touching the theme files by changing user.js and user.scss:
├── _app/
| ├── assets/
| | └── _js/
| | | └── user.js
| | └── _scss/
| | | └── user.scss
| | └── themes/
| | | └── ...
These files won’t be overwritten when you update Almace Scaffolding or update your themes.