Problem/Motivation
We are working on fixing a Group module install problem from existing configuration by using the built-in config installer in this issue. This is complicated story but we managed to eliminate some Group specific issues but it seems there is also an issue in Drupal core. See comment #17.
Steps to reproduce
// TODO Add a minimum code example.
Proposed resolution
Running drupal_flush_all_caches() before SiteConfigureForm.php#L326 solves the problem but we must not use this call because it is a peformance killer.
Speaking of performance... I remembered @Berdir's issue about Do not instantiate entity storages in constructors of services that do not always need them and it seems by only injecting the entity type manager and not the user storage, solves the issue.