Our project has the following configuration:

fladle {
  variant = "internalDebug"

  debugApk = project.provider {
    "$buildDir/outputs/apk/internal/debug/app-internal-debug-universal.apk"
  }
}

Surprisingly, this fails with the following error:

'/.../app/build/outputs/apk/internal/debug/app-internal-debug.apk' not found 

From looking at the code, it seems that if either debugApk or instrumentationApk is not set the plugin will try to locate those files automatically, overwriting debugApk in the process:

Indeed, providing the default path to the instrumentation APK explicitly resolves the issue:

fladle {
  variant = "internalDebug"

  debugApk = project.provider {
    "$buildDir/outputs/apk/internal/debug/app-internal-debug-universal.apk"
  }
  instrumentationApk = project.provider {
    "$buildDir/outputs/apk/androidTest/internal/debug/app-internal-debug-androidTest.apk"
  }
}

debugApk and instrumentationApk should probably be resolved independently to support use cases where one of the values is a custom path while the other is default.