The current work around is to first add the owner to the second list, 'Separate constituent updates into different batch', and then refresh the third. This makes the owner available to add. They can then be removed from the second list.
Steps to Duplicate
Web >> Manage web transactions >> Batch assignment settings >> Event registrations - Edit
Select any item in the 'Batch assignments' list - Edit
Check 'Separate additional revenue into different batch' (The third option)
Choose a batch template
Attempt to add owner that appears in the 'Select owners for batch assignment' list but not the 'Separate additional revenue into different batch' list
Check 'Separate constituent updates into different batch' (The second option)
Add owner to the second list
Refresh the third section by choosing a different batch template.
Batch owner can now be added to this list.