The automapped shared mailbox doesn't send from the shared mailbox by default, even when you are in it. Instead, you can add the shared mailbox directly, using the main credential. But to do this, you have to remove the automap first.
Connect-ExchangeOnline Remove-MailboxPermission -Identity "sharedmailbox@acme.com" -User "mainuser@acme.com" -AccessRights FullAccess Add-MailboxPermission -Identity "sharedmailbox@acme.com" -User "mainuser@acme.com" -AccessRights FullAccess -AutoMapping:$false
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