Were the super admins in src/config.php actually admins? If there were IDs specified there but none of them were actually admins, then this could happen. We have code that tries to prevent the situation where there are no super admins during upgrade, but we trust the config.php value if we get something there, so it doesn't run the code in that case.
Since there were no super admins, that makes me think that it did actually read the value from the config file, but then it couldn't find any of the IDs in the xf_admin table.