What is the Standard Operating Procedure (SOP) to calculate the software license count in compliance for sub level OUs even Pre-shipped OU selected in the configuration?

This configuration is available for each license record. Go to Settings > Compliance > Software Licenses page and click on ‘Reconciliation Rule’ column for a specific license record and enable checkbox “Lend License to Child Business Unit(s)”. Enabling this option allows the license to consider nodes available under the sub level OUs as well. Otherwise, it will just consider the nodes which are available under the selected Business Unit when configuring the license record.