After using the Share Point Processing Wizard permissions on SharePoint Application Pools are not changed.
This is expected behavior.
QMM Release Notes explain:
Accounts listed on the Shared Services Administration page are not processed. The SharePoint Administrator Group Account in Microsoft SharePoint 2003 is not processed.
Possible workaround would be to modify the account manually and use a target account instead.
Ideally this should be an account which was not migrated by QMM and doesnt have a SID History.
It is a good idea to create a new target account manually and then use this account for Sharepoint administration tasks.
The account could be also changed manually on IIS under Application Pool properties.
Attached screenshots demonstrate the Application Pool and the account(s) which need(s) to be changed.
Important: RUM (Vmover) doesnt process Application Pools so when processing IIS via RUM those accounts will remain unchanged.