In attempting to use tests from the theme-tests base that wp scaffold sets up, none of my theme's functions existed. Assuming I was doing something wrong, I created a minimal theme and ran wp scaffold theme-tests to generate the tests. In the theme's functions.php file, I'm simply outputting text to indicate that the theme is loaded. In Travis CI, you can see that when run as single site, the theme is never loaded. When run as multisite, the theme does get loaded.