Acquia Installer Causes False Positives

When a site is installed via the Acquia interface, you're allowed to tell it which packages you want included. When you don't include certain features, the installer doesn't actually put them in the Drupal Core codebase. For example, the core/profiles folders won't all be included and there will be changes in the zendframework and composer files. These folders should either be flagged as warnings instead of errors or the user should be able to select the type of install they have used and features that should be checked for.