For subscriptions including many websites, RA can determine if there are updates on a specified set of websites included in those multisites. Examining only a subset of websites in a multisite speeds up the RA process, and minimizes problems during automation caused by many database copy and backup tasks.
Where possible, avoid installing different modules for individual websites in a multisite. Place modules in the modules/ directory for websites running the current Drupal version.
Note
Websites running the current Drupal version that are created or maintained using Composer do not support the installation of modules for individual websites in a multisite.
Can RA automation work with large multisites? | Acquia Product Documentation
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