[SUPPORT] After running `:project:focus` unrelated projects fail to configure

We're trying to use this plugin in a large repo. However, when the focus is applied, it generates a `.focus` file and `focus.settings.gradle` which appears to have all of the expected projects.

Though, when running `./gradlew clean`, it attempts to configure projects that are *not* in the focus file.

I've been debugging this for a few hours and can't produce a minimal reproducible set. Any help would be appreciated in what to track down. If I hazard a guess, there's some `Plugin` that is pulling in dependencies recursively -- but I am unsure.